Does anyone have any recommendations for niche physical shops that are still open in the Bay Area that are Radio Shack esque, even if small?

If you mean components, I think jameco and anchor electronics are still open. Unfortunately Halted and Weird Stuff are gone.

Urban Ore in Berkeley. It's a salvage shop with an electronics area. Scored some vintage Tek scopes there.

There is also Electronics Plus in San Rafael. It is an old school electronics parts store, complete with the ability to sell you cable by the foot.