This comfortable Bay tour has both indoor and outdoor seating with full narration describing major landmarks as you sail by them.  Boats are dog friendly. Departs from Pier 39 (where the famous sea lions are)

Adult: $30

View San Francisco Bay by Bay Cruise Adventure, a 60 minutes tour that goes under the Golden Gate Bridge, around Alcatraz Island and past Angel Island. It also includes view of the Bay Bridge, North Beach, and San Francisco Financial district. 

Bay Cruise Adventure

a 1-hour tour that goes under the golden gate bridge and around alcatraz!