This was a busy day, San Fransisco City Tour and Alcatraz in the afternoon. I can't remember which company we did the city tour with, booking it online before we left, BUT we did pre-book the Alcatraz tour before we went. The Alcatraz trip has a habit of booking out in advance and I hear of many people turning up on the day and not getting a ticket.
The San Fransisco City Tour took us to many of the main points, a stop at Twin Peaks for the view, Golden Gate Bridge and Japanese Tea gardens.
We had pretty good weather for our afternoon tour of Alcatraz, like I said earlier it's better to book in advance. We had plenty of time to look around before catching the boat back.
The are a number of tours you can find online, I can't recall who we went through but it was a good way to see the broader city
Alcatraz boat trips with Blue and Gold Fleet