17 days in Nicaragus and what to do?

All the places you mention are well worth visiting!

Off 'the beaten track' I'd recommend MIRAFLOR RESERVE and RIO SAN JUAN

Get the MOON Nicaragua handbook.

17 days, you should try to get to the Corn Islands for damn sure. An adventure just getting there via land/boats.

Yes, Moon. On Corn Grande, I stayed at Casa Blanca: very basic, on the beach, edge of town, about $5. Good place to drink Bufalo beer and consider the ocean.

You won't be able to get to Corn Island cheaply with so little time if you still want to see all the other things on your list, but it is worth the extra $$$. Don't waste too much time on Big Corn. Try to get the early flight there so you can easily grap the panga over to Little Corn. I don't suggest staying on that side of the island. The swimming blows. Take a walk on one of the 3 or so paths to the other side. I stayed at Elsa's and it was decent. $20 not bad for 2 people. Don't forget to sign up for at least 1 dinner at Iguana's. It is a bit pricey but usually leads to a very interesting evening.
San Juan Del Sur is skipable. I agree about the Rio San Juan but I don't think you will have the time. It's 8 hours from Ometepe on an overnight ferry to San Carlso than another 3 to El Castillo (which is a great town) than 8 more to San Juan Del Norte than back. You can try to get a boat from Norte up to Bluefields but it is not advisable. We managed for $50 each and than nearly lost our lives on the alleged 3 hour trip (actually was 9). Big waves little boat, towing two other empty boats and no lifjackets (or bathrooms which was only a problem for me, the only girl)
One of my fav places is Laguna De Apoyo. I got lost and ended up there for a week and even returned to spend my last couple of days there rather than Managua. Try to stay at Crater's Edge. It is a wonderfly run place and stunning to look at. $11 for a dorm bed. Ann takes amazing care of her quests and all of her staff are local and very kind.
Ometepe is great. Don't let anyone convince you to take a tour to San Ramon Waterfall. I did it and loved it and at my suggestion people I met the next week went 2 weeks after me and after an exhausting hike found a trickle of water. There had been a landslide after I was there and some guides were not telling tourists that the waterfall had been destroyed.
Miraflor was nice but if you go all the way up there you should check out Somoto and the canyon of the same name.
Hope that helps. I seem to have gotten a little wordy.

Yes, skip San Juan Del Sur, swim at Ometepe---ahhhh

Hola, on landing in Managua I'd get to Granada, spend a few days. Granada is central to the white towns of Diria, Diriomo, San Juan de Oriente and Catarina. You can spend a day touring around up there. With the exception of Catarina you won't be bumping into too many tourists. Another day you can bus to Masaya market, Masaya Volcano Park and maybe the fortress of Coyote. Allow for the better part of a day getting up and around Volcano Mombacho. The island archipelago of Las Isletas is well worth a few hours in a lancha. You can get to Isla Zapatera from Puerto Asese as well and see the petroglyphs. In Granada, the night club we prefer is Café Nuit. They have a great crowd, a sprinkling of tourists but, mostly Nicaraguans. The house band is terrific and the dancing in the courtyard under the stars is great. Accommodation recommendations for tight budget in Granada would be The Bearded Monkey (hostel) on Calle 14 de Septimebre, Posada San Jose (hostel) on Calle Sirena, or for a B&B Casa Silas on La Concepcion. When you've had enough of Granada, you'll want to see Ometepe, then shoot up to Leon, and the beach at Las Penitas. Then return to Managua, shoot to Corn Island and back. If you had time I'd include a stay at Selva Negra Coffee Finca outside of Matagalpa. Have a great trip. MC

I wouldn't advise swimming in Lake Nicaragua. They have been making great efforts to clean it up but it is still a little icky. When I was in Nica this past summer pretty much all the hotels, bars, etc.... at Las Penitas had been destroyed by a hurricane. I'm sure the rebuilding is well on it's way but unless you want an entire beach to yourself save one barely open bar (which we did) I would avoid it. Regardless of what you choose to do you will have a great time I'm sure. Nicaragua is a fabulous country with fabulous people.