San Jose is pretty small, so you can see most of the city in three days. You could do a coffee tour outside of the city. There are several walking tours of the city. The owner of Downtown Yoga offers a good one that will show you all the important historical points of the city in a day or half day with a stop for lunch. One place I enjoyed eating at was Caracas Arepa and Juice bar. They offer Venezuelan arepas, good priced traditional Costa Rican dishes, and fresh juices. Whatever you decide, you can definitely see a lot in three days. I was there for two weeks! about 6 years ago
I like this downtown-ish section of San Jose. Lots of shops and parks, I've gone multiple times. You can probably go several blocks in any direction from here (if walking the neighborhood looks bad, turn around and go the other way!). Check out the local places, not the US chains. There are a few museums nearby (and there is something museumish in the National Theatre too).
And I like this park too. La Sabana - http://g.co/maps/efbm8
It's very easy to take the bus from the Park to the Shopping area (down Paseo Colon), the other way is hard (it's one way at the one end). But it's a nice walk too.
Probably not safe to walk around either at night. But maybe by the theater...? almost 6 years ago