West vs East coast (or both) -Yet another itinerary advice post -

With only 2 weeks, I'd fly to RT from SJ to Drake Bay or Puerto Jiménez, depending on how you want to do Corcovado, 5-6 days.
Then back to SJ and head straight to Tortuguero and then south for the remaining time.

Do the Pacuare on your last full day your of the trip, they'll drop you off back in SJ. I'd just go for the full day raft trip, but that's me. It's a great river.

SJ is Ok but don't think I would waste any time hanging around. If you need a night by the airport Alajuela is a nice walking town 10mins. from the airport.

We stayed at jungle hostel Bolita in Dos Brazos de Rio Tigre and loved it but we also did the three day trek to the Sirena ranger station in Corcovado Park. For that you need a guide, permits, reservations... We paid $500 for 2. If that is too much or too much hiking (20 km on day 1, then on day 2 hiking on the trails around Sirena and 20 km back out on day 3) I would recommend a day trip to Cabo Matapalo if you are staying in Dos Brazos. Just because so much wildlife can be seen there, even just walking down the road.

If you choose Drake Bay you can take a boat trip to Sirena in Corcovado Park. Much less hiking involved. And from Drake Bay you can do the Cano Island diving as well. Just be aware that Costa Rica is not known for great diving.

You could combine the Osa with the southern Pacific Coast and maybe Orosi.

Or go with what #1 suggests.

Or choose the Caribbean coast. Go straight to Tortuguero if you arrive early enough. Spend 2 days there. Then Cahuita for a day (or two). The NP has great beaches, rainforest and lots of wildlife. And then Puerto Viejo and the beaches south of PV. We stayed in Manzanillo and we walked to Punta Uva. Both amazing, lots of wildlife. Manzanillo also has a wildlife refuge with trails (but take a guide if you go far). Raft back to San Jose (but I would also just do one day of rafting). Spend the rest of your time in the Orosi valley. We were going to stay in Orosi but never made it. Also check out Tapanti National Park in that area.

If nature is a priority, then the caribe coast will give you this on many levels and a multitude of eco systems, with a focus on Sarapiqui/La Selva, Tortuguero Canals, and Cahuita and Manzanillo-Ganduca. This would be a good 10 days, including some low key days, and diving. Keep in mind scuba diving is nothing special, so don't go out of the way to do it, but Punta Uva is the place to enjoy that activity.

Raft the Rio Pacuare, back to SJ.

Its really not rugged or interesting south of Jaco or Quepos, or Dominical, this ant ire coast is well developed and though there are mountains hugging the coast, from Dominical to Ojochal, its also all nice vacation residence and small developments, some gated...

The Osa on the other had is up your alley. If you have time, and money, hike the LOOP in Corcovado, basing in Pt Jimenez, (Guide/Permit/Reservation required). You need 4 nights for all that, and better be in good shape, day 1 is a 21KM hike and day 2 is a 17 KM hike. Its jungle, not easy nor pleasant, hot and humid, but, raw jungle. Fly here, you don't have time to take land transport.

Otherwise, head to Drake Bay, you get there via a boat from Sierrpe, which is a great way to tner the region, down the river and the out the mouth and down the Pacific coast, beach landing. You can fly in/out of DB too. Allow 3 nights here, and access Corcovado via boat to either San Pedrillo or Sirena Ranger stations.

Per above, there is great hiking in Orosi Valley area, few tourist too...

Thanks for the replies!

So I booked a flight into Puerto Jimenez on the day we arrive. No flight back though. We will make our way back up by bus. That's the plan so far.

If we do not do the multi day hike, would it be a good idea to rent a 4x4 in PJ, first to get to Dos Brazos, and to visit Matapalo - Carate area? Bus / taxi would work too if it is doable.

You can check Solid Rental Car, they are the only agency serving that town/area.

There is a collectivio going from PJ to Carate 4 times a day, about two hours. It may go to Matalapo too, which is a 30 minute ride from main road. Last one departs about 2-230...

You can get to Dos Brazos by taking a bus (only on weekdays) or taxi:

http://www.bolita.org/getting-here.html

I think the public transport to Carate (which can also drop you off at the Matapalo Beach Rd) left Puerto Jimenez at 6 am and 1:30 pm. Coming back from Carate at 8:15 am and 3:45 pm. That was in 2015. Any hotel in the area would be able to confirm. As you are open to hitchhiking... our friend hitchhiked to Cabo Matapalo and back. He said it was easy to get a ride.

If you plan on doing the three day trek (Carate-Sirena-Carate or Los Patos-Sirena-Carate) you might want to consider booking it now. You could wait till you are there (I don't think May is very busy) but Sirena does get completely booked at times. Again, ask your hotel or contact a tour operator in Puerto Jimenez like Surcos Tours, Osa Wild, Osa Travel...

I don't know your budget but if you can afford it you might also consider staying in Cabo Matapalo. We loved Bolita as the setting and trails are amazing. We thought our room was fine but just be aware it is very basic. Here is a website with more information about Dos Brazos (activities, accommodation...):

http://www.dosbrazosderiotigre.com/index.html

I am in contact with Los Mineros for accommodations. They mentioned a 2 day trek from Dos Brazos to Piedra Blanca (5 hours) and from there to Carate (another 5 hours). I can't find any info on Piedra Blanca in Corcovado. Maybe she had her names mixed up with the nearby park.

Thanks for all your help!

I looked at their website and apparently they do have a Piedras Blanca tour and Piedras Blanca is a gold mining village bordering Corcovado:

http://www.losminerosguesthouse.com/#!losminerosguesthousecom/c1nhl

They also offer a Rio Tigre tour but you can actually easily explore the Rio Tigre on your own. Just hike in/through it for as far as you like. Dos Brazos also has a swimming hole. I believe it is a 45 minute hike to get there (just ask). And even if you are not staying at Bolita you can use their trails for $8. Just email Bolita and ask. Bolita has an office in the village and they will tell you how to get to the hostel and they will give you a trail map. The trails surrounding Bolita are amazing. Valleys, viewpoints, amazing rainforest, two waterfalls and jungle rivers... Lots of birds. Also monkeys. We saw spider monkeys, toucans, scarlet macaws, snakes, butterflies, hummingbirds, a laughing falcon (with amazing black face mask), the giant toad, Jesus Christ lizards, lizards with blue tails, parrots, hawks, the red-capped manakin, the golfodulcean poison dart frog, bats, golden silk orb-weavers (spiders). At night we watched the stars and listened to the jungle sounds. In the mornings howler monkeys woke us up. Enjoy!

I'm ashamed not to have looked at the Tours section!
I read a bit more on Bolita. I didn't know it was actually in the jungle. Sounds amazing. Drawback is having to bring all the food; I like the idea of having a few cold ones after a long day. I imagine you still feel immersed in trees in the town itself? Would you absolutely recommend Bolita over a lodging in town?