Getaway,
The best place to anchor is just west of Alcatraz. There is a shallow shelf that extends westward which makes anchoring with the proper scope easy. I always try try to arrive a few hours early so I can pick my spot and get the scope before it becomes crowded. Don't anchor too close to the island though. One year we were very close and the boat was swarmed by kelp flies. They were so thick, we gave the kids empty jars and they were filling them with live flies.
If it's choppy and you are in a small boat, I have gotten away with anchoring inside the breakwater in front of Aliotos where the tall ship is moored. It is very protected and you get a great view of the show. For several years they were running boats out of there due to complaints from the commercial fishermen but we got away with year before last.
Have a great time and maybe we'll see you out there. I'll be in a 20 ft. Proline walk around with a hardtop and vinyl curtains.