In Oakland: Cycle Sports - This is the home of the United Healthcare Pro Team.http://www.cyclesportsonline.com/
In Monterey: Joselyn's - Fast Frank is a great guy and it's a cool shop.http://www.joselynsbicycles.com/
In San Francisco: City Cycle - Iconic SF shophttp://citycycle.com/
In Redwood City: Veloro - Great shop and Gebhard is great to work with.http://www.veloro.com/
There's really a lot of good shops in the SF bay area.....you shouldn't have any problem. You could also try to stop in to see some of the many companies scattered around the area too. Look Cycle USA has their headquarters in San Jose and they have rides on a regular basis. Specialized does as well and are in Morgan Hills.
There's a ton of cycling related stuff in that area. You should enjoy yourself.