They are the nicest, yes.
They are also the most damn incompetent: their capital was destroyed by the Mirelurks.
The Mirelurks.
Mirelurks.
The other three may not be morally as pure, but they are at least more trustworthy in the long run.
Seeing as they are the only one without their own "End Game Achievement", how unintuitive it can be to get into their MQ route and how poor their MQ Act 3 questline is compared to the other three, I doubt it. Beth seems to have just pushed them as a choosable ending at the last moment.
The only thing that is certain is that they will survive and probably become the military hand of the victor.
Supposedly, you can become their enemy during the Institute's quest "Pinned". Did anyone try NOT to convince those Minutemen to stand down? I know Preston becomes hostile if you ever kill a Minuteman.
Seeing as MM's "Destroy BoS" quest is not just a copy-apste of another quest, I am pretty sure that IF the MM endings becomes canon, they will have destroyed the BoS. Not to forget that the BoS wants to conquer the Commonwealth and the Minutemen, who now rule it, won't stand for it for too long.