I'd go up to San Francisco with the Shi, it's not very far (about 40km to the north) compared to every other known location on the West Coast, and I don't like the Hubologists.
If I have to choose an East Coast location, I'll chose The Commonwealth.
If by games and locations in them only:
Fo1: Shady Sands, a peacefull, isolated village, and knowing it's future is a very great place to be.
Fo2: Either San Francisco, or still in Shady Sands, now NCR
Fo3: I can't really chose somewhere in the Capital Wasteland, I'd go with The Commonwealth, but it's only mentioned.
FNV: Vault 21 or The Tops, Ultra-Luxe if someone prevents
Spoiler the canniblism from starting again.