I've also stayed at the Best Western in San Jose.

In La Fortuna, there's a place called Los Lagos.
Several miles outside town (toward volcano).
Nice, w/ heated & unheated pools, water slides, hot tub, trail up mountain to Volcano vantage point, Croc. farm, and lots more. It includes breakfast.
It's been several years, but (during the rainy season) when me & 2 friends went, we showed up, asked their price, and THEN asked to see the room. They took us to the nice rooms, and charged us $80 for the night. Very very nice for the $$. But we came back a few days later after making a reservation, and got the crappy room that the roof leaked in, so shoot for the nice rooms.

Otherwise, in town there are quite a few livable (clean) hotels for cheap ($25 - $50 range).