I allied with BOS throughout the whole play through, have finished the game, and the Institute and Railroad are gone. However I'd also like to kill the BOS, if possible. Is there any way to do this?
@GEnGEr My thoughts, exactly.
There are no actual quests to destroy the last surviving faction, but you can have so much fun mass murdering them at your own risk. Just make sure you save the game before you start the ultimate destruction.
If you want to destroy the BOS when you're with them talk to Preston Garvey about the brotherhood and you will get a quest where you will destroy the airship. I did this but Liberty Prime is still alive.