Here are a few I found.
Hope it helps.

SF Citadel
181 Eddy St
San Francisco, CA 94102
Phone number (415) 626-1746

Good Vibrations
603 Valencia St
San Francisco, CA 94110
Phone number (415) 522-546

Good vibes

My personal fav is good vibrations and I go to the one on Valencia. There's also one on Misssion street and another one on Polk street.

It's not so much BDSM oriented, but I was taken in once by a dom client and we had a lot of fun with him sharing me.  Super hot, but that was quite a while ago.  I might be worth inquiring about.

you should look into stormy leather  

http://www.stormyleather.com/store.asp  

Citadel is a club not a store but has a relationship with Wicked Grounds which is a coffee shop and sex toy store.  Can't speak to either.  

Secrets, like most of the other SF stores around the strip clubs on Broadway, remains in the persona of tawdry, seedy establishment that the local community wishes wasn't there.  Lots of selection but general focus (also lower quality) to titillate walk-ins and overseen by, generally, one disinterested male cashier focused on stopping shop lifters and the video that's running.  

The couple of stores in the Castro - Rock Hard, Phantom and Does Your Mother Know - are a step up in feel, selection and staff and have slightly more BDSM focus.  All the Good Vibrations stores set the gold standard for retail experience - think if Nordstrom sold sex toys.  I believe the chain is women owned and all have bright stores, good merchandising (rather than crowded peg boards), sample units out to examine (but not try - LOL) and knowledgeably, generally female, staff that are very pleasent and well trained. They have some BDSM gear but not oriented that way.

For more BDSM orientation you need to visit Mr S Leather (www.mr-s-leather.com).  It's off the beaten tourist path (5 minute cab / 15 minute walk from Union Square) gay oriented and staffed by knowledgeably, helpful men rather than women but has the best selection of BDSM gear in the city.  It's the retail equivalent of Good Vibrations but with a gay, darker edge.  You won't find metal shackles and manacles, leather hobble belts and hoods, and all other manner of things in such quantity and diversity to fuel your imagination anywhere else in the city.  It's much like previously mentioned Stormy Leather but with a retail presence in SF.  Of course, I'd suggest shipping the steel shackles back home rather than trying to get them through airport security.  If you go, you can walk diagonally across the street to Leather Etc (www.leatheretc.com) which has a good selection of kink, fetish and club clothing for men and women and some BDSM gear