you literally have to run all over the bay area for the best ice cream. bi-rite in SF, fentons in oakland is a classic (that's what i grew up on), etc. etc. and there are a ton of pop-up shops that are using new artisinal techniques, including LNO2 JIT production, small batch fresh and sustainable everything pop-ups from kitchener in oakland (actually founded and run by a friend of mine from high school), and god knows what more has popped up in the years i've been gone.
i can't point you to the best of _any_ food in the bay area because so much of it is so damned good.