My favorite store in the SF Bay Area is Hung Ming in Daly City. Great selection of central american cichlids (although the store is expensive). King Aquarium in San Jose is pretty decent, and Aquatic Life Forms (in Sunnyvale) has excellent service and occasionally has some cool cichlids.
Superway (in Hayward), Family Pets (in Fremont), and Aquarium Concepts (now in Dublin, but I haven't been to the new store) are also worth checking out. 6th Avenue in SF is also cool to check out if you're in that area.