You can always get a hotel in the Fisherman's Wharf area, they are a little more pricey than other places in the city, but its a good location.
If you do stay at Fisherman's Wharf, you are by (of course) the wharf, Alcatraz, Ghirardelli Square, Ripley's, the Wax Museum, the cable cars (!!), etc.
I've only been around the city in a car (except for the time my friends and I took the BART to Embarcadero and walked around Fishermans Wharf), so i'm not sure how easy it is to get around w/o a car. If you do decide to not rent a car, the BART is a good alternative b/c cabs can get really expensive.
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