A couple of my local favorites: Gravenstein apples and Santa Rosa plums.
My home town, Sebastopol (still counts as Bay Area, right?) is the cradle of the Grav, my favorite apple for cooking, baking and eating out of hand. They have an amazing tart-sweet balance and a great juicy crunch when just ripe. Sadly, they have a very short season—August/early Sept—and don’t keep, but make stellar cider, apple sauce and pies. They are getting rarer as the orchards are replaced by vineyards (or houses), but I have seen them at Oakland and other local farmers’ markets and at Berkeley Bowl, when in season. If you’re up that way, Andy’s Produce—between Sebastopol and Forestville—has a good selection of local Gravenstein cider and sauce. https://andysproduce.com/
And the Santa Rosa plum, developed by Luther Burbank, up 101 in, yep, Santa Rosa. A gorgeous plum and pretty easy to find in Bay Area markets and farmers’ markets, in season. The sour skin makes me pucker, but I still love them (when very ripe, eat over the sink, to catch your dripping elbows). And they make my second favorite jam, after apricot.