Ferry rides on the bay are always great (well-- not if there are huge waves and thick fog, maybe...) On sunny and clear days it's a great way to spend an afternoon. The boats are basic but they do have a bar so you can sip some wine while watching the sunset behind the Golden Gate Bridge or as you ride past other local attractions.
Most people get over to Sausalito, which is really beautiful. Fewer head to Tiburon, which is almost directly across from San Francisco. Tiburon is less crowded and has great views of the Golden Gate Bridge (if you walk down the waterfront park) and the best views of the city-- especially as the sun is going down.
Tiburon has 4 wine tasting rooms (with another on the way) so it's a fun excursion from the city. McEvoy was the first place we stopped. They sell their own wines plus a lot of olive oils, snacks, and wine paraphernalia. That's right on Main Street across from Sam's restaurant.
We headed next to Musette Atelier, which is larger and sells wines from many wineries. The setting is great here and the pours were incredibly generous. We tried 8-10 wines and each one was about a half glass. We were getting so looped we didn't make it to the last of the wine bars. Musette is a great place to stop. Really great woman pouring the wines and a great selection of wines to choose from.
The last wine place is Tiburon Wine, which is a great place to taste wine. They even have seating outdoors on Ark Row-- the cute addition to Main Street that has little shops in historic Victorian Era houseboats (arks) that were moored there and were landlocked when the shallow bay was filled.
If you want to grab some food there, there are a few good options. Sam's is the place to hang out in the sun overlooking the Bay and City and have cocktails (the food's pretty good but the drinks and views are better...) Luna Blue next door has good food and a decent view if you're outside. Salt and Pepper across the street has good food as well, but no view. Tiburon Lodge, just up Tiburon Blvd a block, has good food and a nice outdoor seating area. The best dinner is Don Antonio's, which is in one of the arks on ark row-- no views but cozy Italian food that's really good.
If you like to walk, head either way from the Ferry landing. Right along the green waterfront park will take you to Elephant Rock across from Angel Island. You'll get great views of the Bay, the GG Bridge and the City. If you go left through Main Street and Ark Row, you'll come to the small bay between Tiburon and the small town of Belvedere. The views are great and Belvedere is a really great place for a walk-- narrow stagecoach-era streets connected by long staircases running up the island. There are lots of historic houses and great view spots along the way (GG Bridge, Bay Bridge, Angel Island, SF, etc.-- it's really stunning.)
Enjoy Tiburon!