There are two shops worth going to (but not necessary to buy): Heroes Club on Clement St, and Central Comics and Cards on Geary Blvd. Heroes Club is a notorious shop - started selling Japanese garage kits way back when and has morphed into primarily a 1/6 shop. They have most of the new stuff (mainly licensed stuff, but some military) on display so it's locally referred to as a "museum". Prices are riduclous - expect to pay upwards of twice as much as Msrp or what other retailers are charging - even on new releases. The proprietor has also been the subject of accusations of recasting and ripping off other manufacturers/artists - not sure if valid or not, but wouldn't surprise me if true. Also, the "limited edition figures" the shop sells are just crappy, heavy-handedly weathered and customized versions of otherwise cheap figures. As I said, it's a museum - a good place to see something in person (they get stuff earlier than U.S. distributors) before deciding whether to buy online (for a much more reasonable price).
Central Cards and Comics is a huge comic shop with lots of toys. A large selection of Sideshow and HT licensed stuff. Prices are a bit high, but you may find some rare pieces. Just be careful if you go when school is out or on weekends, as you may be swarmed by the hordes of mouthbreathing Magic Card players that love to congregate in the back of the shop.
If you go to Haight St., there are a couple of cool hipster/vinyl toy shops - KidRobot and Super7 that are pretty cool. They may have a designer 1/6 figure once in a while, but that's about it.
Lastly, if you want some good food, I'd recommend you hit the Ferry Building on the Embarcadero. They also have a farmers market on Saturdays. Stay clear of the Fishermen's Wharf area, unless cheesy tourist traps are your thing!
Have a great trip!