Bizango1, is correct that all three of those are still around. (However, Century Stereo has turned into a mostly Home Theater store unfortunately. Too bad, as I bought my first pair of audiophile speakers there about 25 years ago.)
The Analog Room is highly recommended, especially for anything turntable related, and that includes a fair amount of vinyl. (They have more turntables than any two stereo stores that I know of.) Brian Hartsell, the owner, has been a great help to me in assembling the front end of my system.
Audible Arts is also recommended, but not quite as highly, (but still very much recommended.) Jeff, the owner, is a really nice guy too.
A couple of other audio shops that are close to San Jose are:
Audio High, in Mtn. View.
(A small, but nice, shop).
The New Audible Difference, in Palo Alto.
(This shop was renowned for being very stuck-up and arrogant, at least IMHO. However, they have reopened, after they went out of business, and might have a better attitude.)
Good Luck in your search!!!