Second that recommendation for Spinnaker in Sausalito. It’s higher-end, but ultimately a fine value. The views across the Bay to downtown SF are great but eclipsed by the food. For those views in September, you might want to time your dinner for sunset to see the lights come on in the City. Reservations are wise but seldom really needed.
Check into the Hawaiian Chieftain. It’s a sailing ship that makes Bay excursions from Sausalito. Fun and not too pricey.
Of course you will want to visit the Point Bonita Lighthouse (no charge) in the Marin Headlands:
That’s the head page for California Lights with Point Bonita pictured. Click on "Point Bonita" in the text. It’s open to the public every Sat-Sun-Mon 12:30 PM to 3:30 PM SHARP. You can find a map to the trailhead by clicking on "Marin Headlands":
I just assume you will go to Muir Woods as well. Look on the various maps for Muir Beach and Muir Overlook too, both just a couple of miles west of the Woods.