Our daughter lives in San Fran and when we visit we stay north at Santa Rosa Fairgrounds. Nothing fancy but very reasonable.
We've driven down to Larkspur, parked the car and hopped on the ferry for a scenic ride to Fisherman's Wharf. There we met a small van tour company. We don't typically like to take tours and especially would never do one in a large bus but this one is a small van and the guide was very knowledgeable.
San Fran TourWe spent a very pleasant day with them touring the highlights of the city and then the Golden Gate to Sausalito for lunch and back to the Wharf. Then we took the ferry back to the car. It's an excellent way to see the city. Then if you want to explore in more depth you can drive in on your own.
Have a great trip!