are you in the museum of witchcraft when this happens? Or is it out in the commonwealth as well? Only other time I have experienced that was when a BOS vertibird was overhead and a guy was lobbing mini nukes from it in a prolonged battle with super mutants, if its the museum, then its part of a quest.
Molerat stalker?
Ok, funny aside. It could be a glitch with a molerat following you around. If you try load an earlier save, do you still get it?
its a glitch, have you encountered deathclaws or behemoths? If you have the glitch could be caused by those encounters.
I'd chalked these rumbles and bright flashes up to BoS and Super Mutie Suiciders playing with their mini nukes.