I'm guessing that most FO1 towns are now controlled by the NCR, including the remains of Cathedral and Mariposa, and the Lost Hill Bunker is probably destroyed.

New Reno still exists and the Bishops are still around, but we don't know if it's controlled by the NCR.
Broken Hill is probably abandoned.
NCR stormed Navarro, it's either captured or destroyed.
Redding is probably still around, or at least their mining companies are still around since there's a Morning Star Cavern in NV.

Klamath, Modoc, Ghost Farm, and Den were probably too small to resist NCR encroachment.
Assuming that you got the happy ending for Vault City and Gecko, they might still be independent but they would definitely trade with the NCR.
That just leaves San Francisco. They're isolated and they're technologically advanced so they might have been able to resist the NCR.