My favorite is El Lagarto, an open-air grill that serves huge portions of delicious beef, ribs, lamb chops, shrimp and veggies. Best meat in the area, by far. The restaurant is towards the north end of the beach, right before the long line of palm trees. Tucked away, but well worth the effort to find it. If you can find the Banco Nacional in town, turn left on the next street past it and you'll find a small sign pointing you there.
Yes I left out El Lagarto in Samara, didn't I? We just got back from another annual trip there, and had some of the best steaks I've had in Costa Rica (in nearly 20 years). The Lomito de Res at El Lagarto is to die for - 11 oz. will run you about $18 U.S. with some scant side dishes, but the meat quality, tenderness and flavor is really great. This place is also accessible from the end of the main beach road (about 150 yards north if the tide is not high..... just in case you don't want to trek there by way of the B.N.). They also do very good Snapper a la plancha if you're into fish.
Hi. Kind of depends on "where" in San Jose you'll be staying. (in San Jose central, Escazu, Heredia, Santa Ana, etc.)
As far as Samara, there are a couple of good recs. (See map link) In the past, we've had good meals at Las Brasas (#56) Does an ok paella w/ home made sangria. There is also a place just up the road from the supermercado across from the church (between #51 and #37). Sorry I can't remember the name. Very good meals, especially seafood. Lastly, there was (as of last year) a little place just off the main road (near #53 El Samareno) that did rotisserie chickens, tortillas, cilantro and onions. Nice beach snack.
Hope this helps.