I think I'm stuck between two quests and don't know how to make the game proceed.

I've met the BoS and completed the quest chain up to where Hardin is supposed to depose McNamara (can't help but think of Nip/Tuck with this name.. Where is Troy?) However, everytime I go into the bunker, McNamara is still in charge.

With For the Republic Part II, I'm on the part where I have to "take care of the BoS" I don't want to have to kill all of them, but I don't have any dialogue options with Hardin or McNamara. Am I trying to talk to the right people here? Any help?

As far as i can tell if you get Hardin as the elder there is no way to reach a peacefull solution, so your either stuck with killing the BOS or not using the NCR quests to complete the game.

Also to get Hardin to become elder wait for i'd say a week of in game time then exit the area hes in (go though a load door to another part of the bunker) then go back to where he is, after i did that he was in elder robes and was called Elder Hardin.

If you do need to kill them though get a silcened gun and sneak one shot the elder and the head scribe, then pick pocket the head paladin (who was the securty guy if Hardin becomes elder) then take the keys on them to the self destruct terminal, put on some BOS armor after activing the self destruct because everyone will become hostile, then get out of the base, i'm not sure if theres a time limit but its best not to find out the hard way.

So wait around for a week inside the bunker or outside of the bunker?

I waited pretty much in the same room he was in for close to 2 in game weeks before i finally got annoyed to the point that i went to the other part of the bunker then came right back and he was then the new elder. You just need to wait for a certain amount of time then go though a load door so the game will make the changes i think.