One alternative is to take the train (providing Amtrak is still running in September)from Sacramento to Oakland and then the ferry over to San Francisco.
The tracks are laid right along the margin of the bay, so you will get a feel for the expanse of the waterway system. You'll also get a glimpse of the "Mothball" fleet in Suisun Bay and some of the big ship traffic that transists all the way to Stockton.
That's the best way I can think of. Enjoy the trip.
When you loose control, aim for the cheapest boat