In San Jose, I've stayed several times at the Hotel Villa Tournon, within walking distance of the center of town. Another time I stayed at the Hotel Bougainvillea, way out in the suburbs, which had a larger grounds with lots of good birding.
My top recommendations are:
(1) La Selva research station of OTS. Make reservations through the OTS website www.ots.duke.edu , or call the OTS office at Duke if you have any problems , 
(919) 684-5774
. The rate includes 3 meals and a guided nature walk, then you are free to explore the trails on your own. Some of the trails are off limits and are reserved for researchers. To get to La Selva, go to the Limon bus station in San Jose, on Calle Central near the Hotel Villa Tournon, just north of the little river that runs through town. Buy a ticket to Puerto Viejo de Sarapiqui. There is another town called Puerto Viejo de Limon, so make sure you include the Sarapiqui. Ask the driver to let you off at the entrance to Estacion Biologica de la Selva and walk the 800 meters or so to the station. It takes about 4 hours to get there from San Jose and buses run about 4 times per day. Cost of a ticket is very cheap. Plan to spend at least 2 nights there. OTS also has 2 other research stations which birders can stay at, but La Selva is the easiest to get to and the most interesting, in my opinion.
(919) 684-5774. The rate includes 3 meals and a guided nature walk, then you are free to explore the trails on your own. Some of the trails are off limits and are reserved for researchers. To get to La Selva, go to the Limon bus station in San Jose, on Calle Central near the Hotel Villa Tournon, just north of the little river that runs through town. Buy a ticket to Puerto Viejo de Sarapiqui. There is another town called Puerto Viejo de Limon, so make sure you include the Sarapiqui. Ask the driver to let you off at the entrance to Estacion Biologica de la Selva and walk the 800 meters or so to the station. It takes about 4 hours to get there from San Jose and buses run about 4 times per day. Cost of a ticket is very cheap. Plan to spend at least 2 nights there. OTS also has 2 other research stations which birders can stay at, but La Selva is the easiest to get to and the most interesting, in my opinion. (2) Punta Leona Beach Hotel. OTS arranged this one for me. This is a big resort hotel on the Pacific coast on the way to Manuel Antonio. In addition to the beachfront, the hotel owns several square miles of rainforest with hiking trails., so you can do good birding all day without leaving the property. It's touristy, but yet undeveloped. It's a few miles south of Carara National Park, one of the best birding spots in Costa Rica, the best place to see scarlet macaws. Punta Leona offers tours to Carara on certain days, and since there wasn't one while I was there, they arranged for a taxi to take me there and come back for me for $30, which really worked out better since I could spend the day there at my own pace. I couldn't find a website for Punta Leona, but you can make a reservation through hotels.com, orbitz.com, or similar websites. To get there, I took a bus from the Coca-Cola Bus terminal in San Jose. (there's no Coca Cola sign; they just call it that for some reason.) It's on Avenida 3 around Calle 20 or so. You buy a ticket to Jaco,(again, a day in advance if possible) and ask the driver to let you off at Punta Leona. There's a big gatehouse, and the guard will call a driver to come pick you up. It's about 3 miles from the gatehouse to the hotel, through hotel property all the way. A fantastic place.
(3) Manuel Antonio Natl. Park. The small town of Manuel Antonio right next to the park has lots of small hotels. I picked up the bus in front of Punta Leona and went on to Manuel Antonio from there, where the road dead ends. I stayed at the Velabar hotel, which OTS arranged. (www.velabar.com) A very pleasant place with the sound of Kiri te Kanawa singing Gershwin songs for breakfast while I observed white-crowned parrots and such in the trees just outside. The park is small but has lots of hiking trails and beautiful scenery somewhat like the Point Reyes peninsula of California. Saw lots of new life birds there, also a sloth & some other mammals.
