I can see that (not American so freely admit my knowledge of the local geography is going to be patchy and flawed at best). I think Alcatraz would still make a pretty good "set piece" for a game set in the region if nothing else, if for no other reason than its history and reputation. Perhaps it could be the base of a rival crew, or an outbreak site, perhaps somewhere the government had staged Blight research. (Perhaps it was restored to working order in the dystopian near-future before the Blight, and the subsequent unlucky inmates were deliberately infected in their cells and left for observation)
Keeping it in California, but looking at some of the smaller towns and cities, how about Monterery and the aquarium? Drain the tanks and you've got a lot of space to work with as a location; some medical supplies for veterinary care; right by the sea so fishing is an option, plus the structure would be pretty solid due to the amount of water etc it's built to take. Plus Monterey is a way smaller population centre than Los Angeles or San Francisco, so it's way less likely to become a horrific Vector nightmare (followed by a slightly less horrific Casualty nightmare) meaning an enclave might plausibly last a lot longer. Also, otters! Otters are great for restoring Humanity.