Take the San Francisco Bay Ferry to Alameda Main Street. You catch the ferry from Gate E which is on the right hand side of the Ferry Building at the base of Market Street as you’re looking towards the water.
The ferry schedule is below. The fare is $6.40 one way to the Alameda Main Street stop which is the first stop after leaving the Ferry Building. Buy your tickets as soon as you get on board.
On weekdays the Harbor Bay Ferry is a nicer run. The fare is $6.70 one way and the ride is about 30 minutes. Sit outside on the back deck for a nice view.