The KOA in Petaluma would be a good choice. We live 80 miles from S.F. We take our 5er to Petaluma. Hwy 101 is just few miles away. We pick up 101 follow the signs to Tiburon (a wonderful little sea coast community) about 45 miles. We park our truck in Tiburon and grab the Blue & Gold Ferry that takes you to Pier 41 at Fisherman's Wharf in S.F. (A very iconic part of the city).The ferry passes Angel Island, gets you really close to the Golden Gate and passes near Alcatraz . On a clear day you see the entire landscape of the city along with a wonderful view of Golden Gate and Bay Bridge. It's a great way to see the city without the fuss of driving in the city. Fisherman's Wharf has lots of restaurants and from there you can walk around,soak up the aptmosphere,walk to catch a trolley ,hail a cab or public transportation, and then choose the time you would like to return to pier to take the ferry back to Tiburon. I believe the ferry runs later on weekends but if you go to www.blueandgoldfleet.com you will find the schedule for Tiburon/S.F.
A couple,of precautions. If I remember,the first ferry during the week doesn't depart until 10:30 or a bit later. That's good. Allow yourself at least twice the amount of time you think you need to drive there. Commuter traffic on 101 is heavy during the week so sometimes you are driving at a snails pace. We always allowed a couple of hours just to make darn sure we got there in time,and if we were really early we just purchased our ticket at the ferry building and then walked around a bit. Sept can be beautiful or it can be foggy/cold. We keep and eye on the local weather forecast and pick our day accordingly. The fog will often burn off by the time the ferry departs but wear slacks,good walking shoes,and carry a warm jacket,especially if you want to stand outside as the ferry passes near the Golden Gate. It's powerfully beautiful. We love the city in late Sept and almost always have found a wonderful mixture of fog/sunshine. If you have any other questions you can message me. Petaluma is a great town and it's really easy to get there and to drive through. We spend a lot of time RVng near there and along the N. coast.