We stayed at the San Francisco RV Resort which is south of San Francisco about 15 miles. We ended up renting a car from Enterprise for a few days and they had a location about two blocks from our location. We were also about a $15 cab ride from the nearest BART station. Unfortunately we happened to be there during a BART strike and so the system wasn't that beneficial for us.
I would recommend Alcatraz and you need to book the Alcatraz tour several months in advance. We ended up doing the Alcatraz tour with the added Angel Island tour and I would recommend this option. We also took in an Oakland A's and a Giants game while in town. I would recommend both if possible. Good luck.