It's hard to find a pure hiking store per se. However - many sporting
goods stores do have specialized outdoor equipment that caters to
hikers and backcountry campers. REI is definitely a decent place to
start.
REI
840 Brannan St
San Francisco, CA 94103
(415) 934-1938
http://www.rei.com/stores/sanfrancisco
I like Sports Basement, which has a combination of newer items at a
slight discount with closeouts at a heavier discount. They have one
Potrero location, but I've been to the one at the Presidio (was
formerly a US Army base supermarket) with sweeping views of the Golden
Gate Bridge, Marin Headlands, and San Francisco Bay. There also
plenty of hiking at the Presidio. I threw in The North Face if you're
looking for certain types of equipment.
Sports Basement
1590 Bryant St.
San Francisco, CA 94103
(415) 575-3000
http://www.sportsbasement.com/pop_ups/directions/code1_Bryant.htm
Sports Basement
610 Mason St.
San Francisco, CA 94129
(415) 437-0100
http://www.sportsbasement.com/pop_ups/directions/code3_presidio.htm
The North Face
180 Post Street
San Francisco, CA 94108
(415) 433-3223
http://www.thenorthface.com/na/store-locations.html
If you mean in the San Francisco area in general, I'd put in a word
for Wilderness Exchange and Marmot Mountain Works in Berkeley.