Yep, Gryphon is excellent, I grew up in the neighborhood, that's where I saw a Rickenbacher A22 for the first time
San Francisco itself is, in my humble experience, perhaps a bit dry on steel guitar. I lived there and played in a few bands from 2001-2007, and I think I saw one pedal steel player at one show (the Mother Truckers, iirc), and I never saw one lapsteel played by anyone in that time. Laptops, on the other hand, seems like every other band has one by now, am I right?
Real Guitars is perhaps the most excellent vintage/used guitar shop in all of SF, jammed full of surprises and treasures, and they're really laid back and friendly. I would say they are the best place for vintage gear in the whole city. The only thing is, last time I was there was years before I got into steel, I wouldn't have known a B6 from a B3 back then, so I cannot recall if they had steels or not. So maybe call ahead. The shop is halfway down a funky little side street, behind a very nondescript door, but definitely worth seeking.
http://www.yelp.com/biz/real-guitars-san-francisco
15 Lafayette St
San Francisco, CA 94103
b/t Minna St & Mission St in SoMa
Phone number (415) 552-3310
Mon-Sat 11:00 am - 6:00 pm
Also, not strictly in the city, but another true gem is Players Guitars in San Rafael. The proprietor, Jim, specializes in non-Fender/Gibson brands of vintage gear: Supro, Harmony, Kay, Airline, National, Valco, etc. Jim is worth a call for sure, he's a fella who knows where find anything within a hundred miles.
http://www.yelp.com/biz/players-guitars-san-rafael
844 B St
San Rafael, CA 94901
Phone number (415) 453-8531
Ties-Sat, 12-6