There are several options for San Francisco Bay cruises. There are short 1-hour cruises, longer cruises to more sights, dinner cruises, sunset cruises, and sailing cruises.
San Francisco is a port city, so a tour on the water is a great way to see the major attractions. Cruise under the Golden Gate Bridge and around Alcatraz Island. See sea lions and other wildlife.
The Red and White Fleet has operated since 1892. Boats depart many times a day from Fisherman's Wharf. The "Golden Gate Bay Cruise" provides views of the skyline, Golden Gate Brige, and Alcatraz. The "Bridge 2 Bridge Cruise" goes all the way from the Golden Gate Bridge at the edge of the Pacific Ocean to the Bay Bridge in the heart of San Francisco. They also offer sunset cruises and twilight cruises.
The Blue and Gold Fleet offers day cruises under the Golden Gate Bridge. They are 60 minutes long and go by the Pier 39 sea lions and the San Francisco Bay waterfront. Their 90 minute cruise around Alcatraz Island includes stories of escape attempts.
Hornblower Cruises has San Francisco dinner cruises. A 3-hour dinner and dancing experience. They also have champagne brunch cruises.
For something different, consider an Adventure Cat sailing cruise. Their big, sleek catamaran sailboat offers bay sail and sunset sail excursions. The bay sail is a 90-minute trip past the city's big attractions. If you want, you can help sail the boat.