The choice really depends on what outcome you ultimately want for the Brotherhood of Steel as there comes a point where you must decide whether they should survive or not. The companion "Veronica" is also partly effected by your decision and gives some good insight on McNamara and Hardin.
If you like the Brotherhood of Steel and are planning to side with the NCR, I would most definitely keep McNamara in charge. I think he is a far more diplomatic leader than Hardin and is much more open to new ideas. He's the only one that can offer a peace treaty with the NCR.
Hardin seems to be much tougher and traditional in pursuing the Brotherhood's true purpose. I usually make him in charge whenever I'm aiming for an independent New Vegas.
By the way, looks like you may have posted a duplicate of this topic by accident.
by 
Calendar
