I'm not a dune buggy person, but I highly recommend a bike ride along the bay, up the hill, across the Golden Gate Bridge, down into Sausalito and back to the city by ferry boat. It's easy and a lot of fun. Your son would love it, I'm sure. Regarding staying near the bridge, the old Presidio is there, but there are no hotels right there. The closest is the Fisherman's Wharf area, which is not the "real" San Francisco; it's more about selling shirts, cameras, overpriced food, and junk. I'd choose a hotel downtown and explore the real city. From downtown, you can take a streetcar (the F line) and get to Fisherman's Wharf for a day trip. Or, if you rent a bike near the Ferry Building (there are several nearby), you can get to Fisherman's Wharf by bike easily; it's less then 2 miles, and it's a safe and beautiful ride. Continue over the Golden Gate Bridge and back. The ride takes about 3 hours with a few short stops to take photos. Coming back on the ferry offers great views of the city too!