I grew up boating the San Francisco Bay and Delta. The bay can be treacherous. Pay attention to the markers or you can end up in the mud. You'll want to cruise early and get to your destination before the winds pick up. There is a nice cove at Angel Island next to Alcatraz but it can be packed. There is a fort from the Civil War on the island and some great hiking trails. Of course Alcatraz is a must. There are some places that you have to spend a couple days at. Sausalito, Jack London Square, Pier 39 in San Francisco. Running from Redwood City up to Sacramento is a nice 2+3 day cruise or over to Stockton. Run up the Napa River via San Pablo Bay to do some wine tasting. Benicia used to have some nice restaurants close to the marina. Run up Suisun Slough via Grizzly Bay to Suisun City. The delta has an interesting history. Much of it are still duck hunting clubs. Grizzly Island is where I used to hunt. There are some great little delta towns also with interesting history. You could spend a lifetime exploring the Delta.
Now for my favorite:
The Inside Passage of the Pacific Northwest is incredible! So many islands and coves. Most of the islands have great hiking trails. You could spend another lifetime or two exploring from the San Juan's up to Alaska. Most of it is protected from the open ocean. I bought a trawler and it was delivered to Bellingham, Washington, (a great town). I was planning on immediately running the boat down to Redwood City which, is South San Francisco Bay and my home. I was talked in to spending some time cruising the local area (Washington, British Columbia). As a matter of fact by many of the people on this forum. So I cruised around for a couple of weeks then had to go back to CA to wrap up some things so I could spend more time in the PNW. I ended up staying most of the year and cruised 1300 nm, San Juan Islands, Gulf Islands then over to False Creek, up Indian Arm to Bedwell and over to Howe Sound then up the Sunshine Coast to Pender Cove then up to Cortez Island and Squirrel Cove and much more.
I'm leaving California in less than two weeks to drive back up to Canada (where I left my boat) do it again and hopefully get further North to the Broughton Islands. I don't really care just as long as I'm up there cruising.
The Pacific Northwest is the most incredible boating that I've ever done. I don't know if I'll ever get the boat down to San Francisco. The Delta is fun and relaxing and safe. The PNW is amazing, exhilarating, exciting and protected from open ocean but you have to pay attention to huge tidal changes and passages that can sink a 50' trawler if you go at the wrong time.
I've met so many gracious and helpful people up there. You inevitably start talking about where you're going next and people will warn you what to be careful of and suggest more places to go. This season I'll have an electric bike on board to I can better explore the islands.
Do yourself a favor and check it out. If getting your boat there is not doable charter a boat.