I am investergating some of the local factions as part of the main quest, but which ones should I work with? I want to take out the brotherhood as I'm not a fan and they look like they have some good items to rook. (After learning to wear power armor that is!)

Well if you want to take out the BOS, you can do so working with any of the main 3 factions as they all have a mission to wipe them out. This is one of the few games where being evil is easier than being good, because finding how to incorporate the BOS into any of the factions rather than simply destroy them takes a lot more time, preparation, and character stats.