Many in San Jose use Trail Head Cyclery
in south San Jose near Los Gatos. The guys there are very avid and very knowledgable mountain bikers. (See link for bikes they sell and rides the shop guys do.)
The prices are a little higher there, but I still go there for the great advice. Lars was a good bike racer and will fix you up good with whatever you need. Others in the shop are all good too. They have a great selection of everything.
The only down side of Trail Head Cyclery is their shop has a 3-4 week back log. I don't want to be without a good bike that long for simple repairs.
So I go to Reeds Cyclery
for standard bike maintainance, where I can get repairs in less than a week. They are a good Santa Cruz bike dealer. I bought my Heckler there and have been very happy with their service. One guy there, Jesse, really knows Marzocchi forks inside and out. But they're more of a general sport's shop and don't perfectly fit your request for a "true mountain bike shop".