I'm not sure who I need to talk to to get the NCR and BoS to ally. I've heard that it could be done (I think). I've currently put Hardin in power of the BoS, and as far as I know I've completed all the BoS quests. I'm also on the quest for the NCR where they ask you to destroy the BoS.

If Hardin is the Elder, then a NCR/BoS treaty is not possible.

Dang, then I screwed up...oh well

Yeah, it's definitely best to leave McNamara as the Elder if you are doing a NCR playthrough and don't want to destroy the Brotherhood.

Yeah, you have to keep McNamara in power or it won't happen.
Hardin is more expansionist, and won't even consider the NCR as potential allies.