National Theater followed by Gold Museum
Jade Museum at the INS building
Museo Nacional
Those are ultra easy, short walk ....probably less than 1 mile and you can go at your own pace ....Poas Volcano , shorter walk (from where the bus drops you off of course) Irazu Volcano
San Jose cant be described as a 'nice city' so the options there are very limited
You could also do a tour to a coffee farm
INBIO park is a nice museum where you can see many interesting things about our fauna/flora