The brotherhood is not dead in the west, if you blow up their bunker then it says in the end game slides that the survivors went out and joined up with other chapters. And I actually think it would be cool to see the brotherhood in a dlc, what was that the dlc that was supposed to be coming out called where there is supposed to be a huge stockpile of pre war tech? Sounds like its right up their alley to me. And at any rate the brotherhood is thriving on the east coast after beating the enclave so im sure we'll see them in fallout four either way.
Caesar Legion, according to most sources
The BOS is doomed atleast that they make a truce between the NCR, then again, all California, and techinally, Nevada, are in control of NCR, they will shot them on sight