I lived and cruised
SF Bay for about 10 years. The Bay itself is more or less day cruising. South Beach Harbor near the ball park is a good spot for a guest berth for a few days to explore the city if you're so inclined. Farmers Market at the
Ferry Bldg, venture further down towards fisherman's wharf to the maritime museum, etc. Good access to the city from South Beach.
Drakes Bay is awe inspiring. But it's pretty
remote and desolate. You could
head north to Tomales Bay, but too is pretty spartan.
Prettiest anchorage in the Bay is Clipper Cove at Treasure Island. Difficult to get off your
boat there but it's a really relaxing anchorage.
Jack London Square on the Oakland side of the Alameda Estuary is another nice day stop. My info is dated so check Active
Captain, but they used to have short term Docks and a Saturday farmers market and several decent restaurants within easy walking distance.
For
anchoring in the bay, we enjoyed
China Camp. Shallow
water and currents run strong, but a cute shoreside museum of how the Chinese fisherman used to life and earn a living. There are also many nice trails nearby. We preferred Petaluma to Napa but do check access - silting has been a problem. Not even sure you can all the way to Petaluma anymore.
But if I had 2 weeks in
SF Bay, I'd
head up the
Delta. Once north of Rio Vista, the towns get smaller and the
water gets narrower. Benecia is a good stop along the way. Our favorite towns were Locke and we also like Rio Vista. Sacramento has city Docks that are very convenient, but it's a long way and you must time tides/currents. We found many side sloughs along the way where we'd tie up beneath a cottonwood and just read. It's not beautiful or anything, but it sort of crept under our skin over time.
Hal Schell wrote the definitive cruising guide to The Delta. He passed away many years ago and unfortunately his book is long out of print. But it has many stories and historical facts. If you can find a copy, even at a premium, you will enjoy it if you head up the Delta.
Good luck. And I look forward to other contributions.
Peter