Hi Java Man --
Welcome!
There is Diver Dan's in Santa Clara that has already been mentioned -- I have checked them out, and was disappointed in the reception I got at their shop -- I just didn't 'click' well with them.
My husband did his certification (at least up to the referral point) with Diver Dan's -- he also wasn't impressed, but managed to complete the skills and academic work. At the time they were training using the San Jose State University pool.
I have used Captain Aqua's which has a location in Dublin and in Hayward. They use the San Ramon (High School - I think?) Pool. I have bought gear from them and have been able to accompany them to the pool to check out the gear. However, I have not been overly impressed with them either.
I have not been able to find any other dive shops in the east bay.... so, I have been relying on Maui Dreams Dive Co -- yep, my "LDS" is 3,000 miles away!
Let me know if you discover a dive shop extrordinaire!
Liz