There isn't really a way to side against the NCR _with_ the Brotherhood -- Instead, you have the following options:

- Broker a truce between the NCR and B.O.S.

- Destroy the B.O.S.

- Ignore the NCR quest to destroy the B.O.S. and side with a different main faction (Yes Man or Legion, since House is taken care of at this point), while continuing the B.O.S questline

To broker a truce, you must **not** have ousted Elder McNamara during the quest _Still in the Dark_. When the NCR gives you the quest to destroy the B.O.S., and you've finished _Still in the Dark_, go talk to Elder McNamara and tell him that the Brotherhood wants to destroy them. That will prompt McNamara to propose a truce. If you've finished _Still in the Dark_ and Elder McNamara won't talk to you, try waiting outside the bunker for 2-3 days, then re-entering and talking to him again (known bug). 

If you ousted McNamara, the only way to make a truce between the B.O.S. and the NCR is through the following console command, which makes the game think that the Elder offered a truce: `SetObjectiveDisplayed 136166 56 1`