With the best natural bay in the world, San Francisco has a rich maritime history, and getting out on the water is one of the most exciting ways to explore the area :)
The Marin/north side of the bay generally has warmer weather and more protection from currents. Sea Trek in Sausalito rents kayaks and paddleboards, teaches class and leads a variety of tours. Angel Island is a great trip (with camping, if you plan ahead!), but it's hard to go wrong when the weather cooperates.
Spotting wildlife is nearly certain - and very occasionally a whale! - as is getting wet :)
Address: 85 Libertyship Way, Sausalito
Website: http://www.seatrek.com/