From the ferry terminal, you can take the ferry across the bay to Sausalito, Tiburon, and Larkspur. View are spectacular on a beautiful day. On a cold day, it's pretty miserable outdoors.
This is a great way to go to Sausalito for their Art Festival or just for lunch while enjoying the San Francisco Bay scenery on the way. The ocean breeze on a clear summer day or a mystic sunset over the Golden Gate Bridge is well worth the ride! Hold on to your hats and kids at the front seats of the ferry!
And the Ferry is the cheapest way to get out on the Bay. You can make it even more of an adventure by biking to Sausalito/ Tiburon and ferrying back. Point out landmarks such as the Golden Gate bridge, Alcatraz, Angel Island, Mount Tam, the Bay Bridge, the city skyline. Also visible include Berkely (see Sproul tower?), the Port of Oakland (and George Lucas's inspiration for the AT-AT walkers from The Empire Strikes Back) the Richmond refineries and Yerba Buena/ Treasure Island (the latter created from the earth dug out to build San Francisco's skyscrapers).