Hi - We went last summer to California, and to San Francisco for a few days. We booked the top tour, inclusive ticket - tour of the city in the morning and we were dropped off at the pier to get the Alcatraz ferry in the afternoon. I would recommend booking in advance, as there was a huge queue trying to get on a ferry without advance booking. It is well worth it - very interesting. I would also recommend the bus tour of the city too - very good. Try www.allsanfranciscotours.com to book tickets online.
Have a great time.