Hotel Grano de Oro.
Not cheap but good value with all things considered. Best breakfast in the country for 4-6k (depending on what you order, the huevos rancheros are great) with exceptional coffee (unlimited) and a fresh juice of your choice included. By far the best atmosphere also.
I don't know if I would call it a full on 'brunch', but they serve breakfast at least until 10:30, and maybe later on weekends. Its not that far from the gulch either, near paseo colon.
http://www.hotelgranodeoro.com/Agree. Best breakfast in San Jose hands down. Great food in general actually, but bring your wallet for dinner.