Costa Rica: I loved the Cahuita National Park (nice beaches, rainforest trail and lots of wildlife) and the beaches south of Puerto Viejo (we stayed in Manzanillo). I also loved the Osa. We did not hike the loop (Los Patos-Sirena-Carate) but we hiked from Carate to Sirena and back to Carate. We spent two nights at Sirena and saw lots of wildlife. The problem is that since the Sirena ranger station has been renovated it has become even more expensive. You need a guide, permit, reservation at Sirena and you can't take your own food any more. The food at the ranger station is good but expensive. We paid $500 for the three day trek for two people in 2015 but I hear it is now at least $700. Going to Drake Bay is an alternative if you really want to go to Corcovado as you can reach Sirena by boat. Day trips are $90 but staying overnight at Sirena (best time to spot wildlife is dusk and dawn) is much more expensive. You could also choose to go to the Puerto Jimenez area and not enter Corcovado Park at all as you can see lots of wildlife without even entering the park. We stayed in Dos Brazos de Rio Tigre at an amazing rainforest hostel (Bolita) with great trails. Lots of wildlife in Cabo Matapalo and Carate too.

In Nicaragua choose a few volcanoes to hike. Ometepe Island has two. Both tough climbs. Ometepe also has nice lake beaches, a waterfall, a natural spring pool, a nature reserve, kayaking... Don't miss volcano Masaya (very active... you will see a lake of lava) near Granada. Leon is a great colonial city. Hike up volcano Cerro Negro and board down. Do the overnight volcano Telica trek (very impressive crater and spectacular sunrise). Las Penitas/Jiquilillo for beach, surfing, nature reserve, sea turtles... Esteli for Somoto Canyon and hiking in El Tisey and Matagalpa for hiking and coffee (Cerro Apante, Selva Negra...). Rio San Juan: Los Guatuzos for wetlands, rainforest, wildlife. Hidden gem: Chocoyero-El Brujo near Masaya: waterfalls, trails, birds, wildlife.

Guatemala: volcano Acatenango overnight from Antigua (make sure you are acclimatized). Lake Atitlan: Solola market (not far from Pana, Tuesdays and Fridays), Santiago (go see Maximon), walk from Jaibalito to Santa Cruz and maybe on to San Marcos. Xela: volcano Santa Maria, volcano Tajumulco overnight, hot springs. Nebaj for hiking. Lanquin and Semuc Champey. Tikal (stay overnight at the park in a hammock) and Yaxha.

Honduras: I have only been to Copan. Great ruins, nice town.

Unforgettable... Costa Rica: seeing tapirs and a puma with two cubs near Sirena (Osa). Sunrise and toucans at Bolita (Dos Brazos, Osa). So many sloths in the Cahuita NP (and eyelash vipers). Nicaragua: standing on the very edge of Telica's crater. Giant iguanas falling from trees in the water while we were kayaking in Los Guatuzos. Helping release baby sea turtles into the ocean in Jiquilillo. Guatemala: my husband proposing on top of Acatenango at 3 am while Fuego was erupting. Banana bean balls at the market in Solola. Being squished together in a Guatemalan camioneta with a Maya lady and her baby while she changed the baby's diaper with the baby's head on my lap. Maya people praying and chanting on top of volcano Santa Maria. Sitting on top of the bus while leaving Lanquin at sunrise. And much more...

Wow, 9 months. Lot of research needs to be done.
What do you and you daughter like to do and see? What are your interests?

Right now thinking:
1 Month - Costa Rica, the Caribe side, safe easy swimming, great jungle and wildlife, safe small towns, easy cheap stuff to do. Dump Manuel Antonio, pricey and touristy.

3 Months - Nicaragua, land cross from CR, cheap country with lots to do, good towns, ocean and people. Ometepe is fantastic.

3 Months - Guatemala , fly from Managua.

2 Months Mexico - either the Yucatan, for the Caribe and lots of other stuff or Chiapas for more culture and lot of other stuff..

Granada: just wander around and see the main sights. The central park, a few churches (I like Guadalupe on Calle La Calzada, the street with the restaurants), don't miss the view from the bell tower of La Merced, the San Francisco museum with the zoomorphic statues, stroll through the market, have lunch at El Gordito in the central park (try the vigoron)....
Boat or kayak trip through the isletas.

Late afternoon/early evening visit of volcano Masaya. Very active right now. Only short visits allowed but you will see a lake of lava.

Volcano Mombacho: cloud forest, trails, nice views if not clouded, birds and hopefully other wildlife as well

Laguna de Apoyo: crater lake. Great for swimming, kayaking, walking, wildlife.

The white villages: Catarina (great viewpoint of the lake), San Juan de Oriente (pottery)...

Chocoyero-El Brujo: waterfalls, trails, birds, monkeys and other animals... best at dawn or dusk to see wildlife. We stayed overnight.

Another option would be Leon instead of Granada. Great colonial city (churches, museums, murals...). Great volcanoes (Cerro Negro, Telica). And Las Penitas: nice beach, fun waves, nature reserve.

Or one day for Granada and then Ometepe Island for 3 days. Dramatic island with two volcanoes (one active and one with cloud forest), lake beaches, rural communities (homestays possible), nature reserve, wildlife, natural spring pool, waterfall, kayaking, petroglyphs, horseback riding...

Without knowing the rest of your travel plans it is hard to give advice. San Juan del Sur has a pretty bay and great sunsets but it is true that the beach in town is not the best. It is also a party town but maybe that is what you are looking for. You can commute to the better beaches north and south of SJDS. Or stay there. There are better beaches in Costa Rica and Nicaragua. I like Ometepe Island a lot so I do hope you have time to go there as well and that you have time to explore other parts of Nicaragua.

As for going from SJO to SJDS. You could go to Liberia and visit Rincon de la Vieja. We liked the fumaroles, boiling mud pots, hikes, waterfalls, swimming holes... You can take a bus to Liberia and then get your hotel near Rincon to pick you up, take a taxi or take the bus to Curubande. From Liberia you can take a bus to the border. Then a taxi to SJDS or a bus to Rivas but get off at La Virgen and flag down a bus there to SJDS.

The ferry from Granada to Ometepe is not running, and has not been for some time.
For now you will need to take a bus/taxi/shuttle from Granada to San Jorge (about an hour trip) and take the ferry from San Jorge to Ometepe.

As for the boats from/to Los Guatuzos. Here is information from the Moon Guidebook
From the west dock near the CANTUR office in San Carlos, colectivos leave for Papaturro Monday-Wednesday and Friday 9am (4 hours, $4 pp); the trip stops at the small island of Chichicaste, where fried fish and soup are available ($2). The boat returns to San Carlos Monday, Tuesday, Thursday, and Sunday, leaving Papaturro at 8am. The fast boat ($6) takes half the time. It leaves Tuesdays and Saturdays 10am from San Carlos, returning Monday and Friday 9am. Or you can rent a private panga ($120), which can take up to 10 people to Los Guatuzos in only 1.5 hours.

I definitely agree that you could skip Managua. I would swap in some time in Leon as well. It's a beautiful city with loads of museums. For monkeys, you might see some on Ometepe on the volcano hike but other than that you should try either a trip down Rio San Juan or Matagalpa.

Matagalpa will probably be easier with a kid and is actually a really nice city with a coffee background so you could visit a farm like Selva Negra and get a full tour of how they make coffee as well as a tasting. They have some nice nature hikes on the property and I saw loads of monkeys there, more so than Mombacho.

Los Escapodoes is a lovely glamping option on Big Corn. They have amazing views and it's run by a sweet Aussie guy and his cute dog. http://www.losescapadosecocabins.com/
Little Corn is great but the boat ride can be rough and I concur that only the front stretch has a paved walkway. The rest of the island is dirt paths or no path at all. You shouldn't let that deter you though, just be aware.

San Juan is fine but if I had two weeks I would choose a less expat heavy town. The beaches recommended by others are good options. You will basically feel like you are at home in San Juan. Think Playa Tamarindo in Costa Rica but a lot more drunk backpackers. Steer clear on Sundays as they have their Sunday Funday drunken extravaganza. You are going to have a lot of beach time anyway on the islands so you could potentially skip it and spend more time in the other towns so you don't feel like you're rushing.

Other spots to consider:
Somoto Canyon - you could do this as a day trip from Matagalpa or stay the night before or after.
Laguna de Apoyo - beautiful warm water lake very close to Granada - you could do this as a day trip as well but there are some lovely well priced places to stay along the lake. If you get up early enough you can see monkeys around the area and there are lots of other animals hanging around

Enjoy your trip!

P.s. Here are some posts from my blog in case you want some more detail on Somoto Canyon: https://www.tofutraveler.com/blog/somoto-canyon ; Laguna de Apoyo: https://www.tofutraveler.com/blog/laguna-de-apoyo-resort-for-budget-travelers ; and the Corn Islands https://www.tofutraveler.com/blog/corn-islands-nicaragua

Thanks so much for all the input all! After reading the suggestions, we've decided to scrap the Costa Rica idea and just do Nicaragua. So in that case, wondering if we'd have enough time to do corn island? Total is 16 days, and our musts are Leon, Granada, Ometepe, and San Juan del sur, and then corn island if there's enough time. Is Granada something we could just do 2 nights and that would be enough?

Nicaragua has everything you want, with the exception of hot lava. but one week is really tough. I'll give you 2 itineraries:

1) Granada, Ometepe, San Juan del Sur

Granada is the beautiful colonial city, and from there you can visit volcanoes like Mombacho and Masaya, which are more drive up volcanoes, but still great. Ometepe is my favorite destination in Nicaragua, a place where agriculture is still mostly done without machinery. For San Juan del Sur you'd want to go to one of the surf camps outside town, because the beach in the SJDS town is a bad one. The good thing about this itinerary is that everything in this region of Nicaragua is close together, so you spend very little time on transport.

2) Leon, beaches at Poneloya/Las Penitas, plus Granada at the end, or nix Granada and do the Somoto canyon in the north of Nicaragua.

Leon is a great historic city too, more politically correct than Granada, and you can hike the best volcanoes from there, like Telica, or Cerro Negro for the volcano surfing. The great beach towns (better than SJDS) are only 1/2 hour by bus from Leon. Somoto canyon would be great for teenagers, and can be done in 1/2 day's time. But the transport to get to Somoto takes 4-5 hours one way from Leon.

Unfortunately I can't see a way to combine Leon + the beach + Ometepe in one week's time.

You can get around ok by local transport. Car is better. You can rent in Granada or Managua and return after the ometepe part. Not all that expensive. Ferry takes car over. Make reservations which you do not need to do if you do not have car.

Since you're intent on San Juan del Sur, why don't you start there and check out Nicaragua namely Isla Ometepe? You might change your mind about the other places. And when is "coming up"? I'm thinking sea turtle hatching/nesting.