Keeble and Shuchat in Palo Alto - although not the equal of B&H, it's probably the best in the Bay Area. It's about 5 minutes from Mountain View on California Street.
http://kspphoto.com
In San Francisco proper, the best are Adolph Gasser and Calumet photo. But K&S has a more comprehensive lineup of new and used gear, pro and amateur.
Edit: I just saw that Samy's which is the largest photo store in L.A. just opened a San Francisco store on Bryant Street.