For SFO transit, check 511.org, which will tell you how to get anywhere from anywhere in the Bay Area.
Basically, BART goes from right inside the international terminal to downtown SF (and beyond) for $8.25. I'd get off at the last SF stop, the Embarcadero, and then take either a bus or tram to the wharf area.
There are some nice hotels in that area, but it's all very touristy and honky tonk. North Beach (Little Italy) is walking distance (up Columbus), as is Telegraph Hill, Chinatown and, a little further, Union Square.
Best time of year to be in SF (I am now, too, but returning to Budapest in two weeks).
Last edited by Mark in CA; 10th Sep 2012 at 22:21.