Oh, great timing! September is a wonderful month to visit.
I would bring sweatshirts with hoods, just in case. You are coming at the best time so hopefully the weather will be beautiful.
we definately enjoyed the night tour of Alcatraz . . . an added element of eerines and a great view of the city lights. Definately wait until you are ready to leave the city to pick up your rental car - parking is a beast.
How much time would you allow? Our boys are 15.5 & 12.
We'll be arriving at SFO late the night before and our airport hotel (Embassy Suites) offers a free trolley to pier 39. Is it walkable from there? I'm considering holding off renting a car until we head off to Yosemite.