I like the Minutemen winning because it's fun imagining the good guys winning. But the Brotherhood winning better aligns with Fallout's vibes, and I think it makes the story more interesting.
I think given the amount of detail put into the Brotherhood that it's very likely to just be them. Liberty Prime is reassembled and the Institute is gone. Synths as well. The Railroad has no reason to exist (not that they survived the onslaught).