With one of the world's best natural ports, San Francisco owes much of its prominence to oceanic travel and Maritime Museum is a great visit for history and maritime buffs. The Balclutha, a tall sailing ship from 1886, is the crown jewel of the bunch (7 total). The USS Pampanito submarine/museum is run by the same organization, but a few blocks away on Pier 45.
There are a lot of events, the Chantey Singalongs are especially popular, check the calendar!
Otherwise, there is a small indoor museum on Beach St nearby, and the Aquatic Park itself offers excellent views of the bay (Golden Gate Bridge, Angel Island, Alcatraz, etc) and is a great walking tour... or swimming (!) for the brave.
Website: http://www.nps.gov/safr/planyourvisit/events.htm
Wikipedia: http://en.wikipedia.org/wiki/San_Francisco_Maritime_National_Historical_Park
