I eat fish nearly every day, so here is my take on seafood in San Jose. The great thing about the fish is that, for the most part, it's local, reasonable, and usually a great value. I recommend you leave your american food habits behind for a day or two and try local ceviche, pescado entero, al ajillo, etc. enjoy the taste of this country.
In Sabana, Curridabat, Moravia and Alajuela you can find Princesa Marina. This is a famous local place which specializes in whole fish, with or without the bones, with or without relleno (seafood filling). They have everything from the sea! Also beer and booze.
http://www.princesamarina.com/rests.htmlPeruvian style ceviche, corvina, tiradito, pescado a lo macho at:
Soda Perú by Zona 2 (closed weekends I believe)
Machu Picchu of Paseo Colon (across from Oasis) and in San Pedro. The former is best.
Segundo Muelle in Sabana. Very pricey and trendy. Dress up for this one.
Surprisingly good ceviche at:
Sportsmans
Central Pub on Paseo Colon
Nice informal sit down place in La Uruca is La Fuente de Mariscos. You need to take a cab there and a good place to take a Chica unless she's from La Uruca (then they might see some one they know. Not always cool).
And my favorite.....
Soda La Conquista in Mercado Central. They have very fresh fish and lots of variety. A fun and healthy lunch option. They take credit cards, offer fresh juices, and entertainment in terms of people watching. Try their chuchecas, a freshwater clam ceviche served in their black ink. Also the whole fish (pescado entero). Comes with head, eyes, fins, everything crunchy and edible. Their sopa de mariscos is terrific.
I've also had numerous casados con pescado at sodas around town and in the food courts at the San Pedro and Plaza Mayor malls. All usually very good. Served with black beans, white rice, salad, and maduros.
If you're a fish lover like I am, San José, Costa Rica is tuanis.