After going on the BoS ship and listening to the masters speech and talking to him (what a svcker!) I blew his head off and killed the rest of the invaders on the ship. Then I did the same at the airport and police station. But NPCs all over still talk about the BoS as a threat, and I got a BoS vert at the Glowing Sea.

Is there a way to destroy the ship or better yet take it over? I just want everyone to stop worrying about an invasion.

I'm guessing that the Railroad guys may have a mission to rid the wastes of the BoS. I could be wrong though.

I'm level 32 and haven't had a single npc mention the word "railroad".

Apparently you find them if you follow the main quest line.