The Alameda / Oakland Ferry is a good way to get into the city from the East Bay, though a bit more expensive than BART at $11.00 round trip for adults. A full service beverage and snack bar is included. Bicycles can be brought along.
The ferry’s ports of call include Jack London Square, Alameda, the San Francisco Ferry Building, Pier 39/Fisherman’s Wharf, AT&T Park, and Angel Island. At present there are 13 trips a day between Jack London Square and the Ferry Building; the full schedule is here.