I'll be the first one to tell you that the NCR has a lot of problems at its core, but at the same time I think they have the best chance at helping the country recover morso than the Legion, and definitely more than the Brotherhood. The only other organization that I think has just as good or even better direction is Lyons Brotherhood on the east coast.
I want you to see this. Im going to offer you the "red pill". If you want the "blue pill" look away and dont read this post. This may sting a little.
According to the Vault, the BoS leadership's Karma is listed as "Good" (even Hardin) and the NCR leadership's Karma is listed as "Neutral." Even Ambassedor Crocker, the dove, is Neutral.
BoS - Elder McNamara
Karma: Good
http://fallout.wikia.com/wiki/Nolan_McNamara
BoS - Head Paladin Hardin
Karma: Good
http://fallout.wikia.com/wiki/Edgar_Hardin
BoS - Senior Knight Lorenzo
Karma: Good
http://fallout.wikia.com/wiki/Lorenzo
BoS - Paladin Ramos
Karma: Good
http://fallout.wikia.com/wiki/Ramos
NCR - General Oliver
Karma: Neutral
http://fallout.wikia.com/wiki/Lee_Oliver
NCR - Colonel Cassandra Moore
Karma: Neutral
http://fallout.wikia.com/wiki/Cassandra_Moore
NCR - President Aaron Kimball
Karma: Neutral
http://fallout.wikia.com/wiki/Aaron_Kimball
NCR - Ambassador Dennis Crocker
Karma: Neutral
http://fallout.wikia.com/wiki/Dennis_Crocker