If taking the night tour, make sure you pay attention to the closing time of the parking structure you choose. We got shafted by a place that closed at 7PM when the tour started at 6PM. We were even asked by an employee as we were leaving if we were going on the night tour of Alcatraz (which takes 2-3 hours). When told that we were, he said “oh, its great” and continued on. Nothing like “well, you realize we close in an hour, right?” We returned to the place locked up and our car unreachable until the next morning. We did end up sneaking it out and leaving cash in the attendant’s booth with the help of a little “social engineering.”

Point being, San Francisco, while having great tourist attractions, doesn’t have a parking system that tends to cater to the tourist. Beware.