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.

Anchor is the only one left.

Fond memories rifling through HSC back in my Cisco days :(

American Science and Surplus .. I think … still exists in Chicago.

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

Oh! I have been there but I was only focused on house / remodeling type stuff, thanks for the recommendation!

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.