There is Free parking in the wharf area. It goes really quickly though. I was able to park at Boudin Bakery and Cafe. We ate lunch and walked the rest of the Wharf to the museum and looked at the boats. If it is full, you can park downtown and take the trolley. Thats what we did the day before we toured the ships. We parked for $12 all day close to the Mall area and caught the Cable Car to the wharf.

First, you can park along the street but the problem is it is 2 hours at a time so you have to feed the meter at 2 hours. It might be better to park in a lot. This place is cheap and not along walk to pier. Imperial Parking (U.S.), LLC Fort Mason Center 2 Marina Boulevard San Francisco, CA 94109 4 hours is $10.