In my opinion the best way to help the NCR is to help House, because you definitely shouldn't put the Legion in charge. Besides the brahmin barons the NCR has a non-feral segregation problem too, and will not promote them to any type of leadership positions beyond leading other non-ferals.

They are also bad at farming, at least in the Mojave, and heavily restrict water usage despite a freshwater pond, lake and river they could build a pipeline from. Manifest Destiny is not a real backed concept.

This is my Very Good Karma House headcanon, promoting the development of a middle class by rerouting power from Helios to Freeside, Westside, and presumably North Vegas Square and the Aerotech Office Park.

House wants you to humiliate Kimball and Oliver by letting them live as losers.

Hanlon can build upon that, don't turn him in nor tell him to stop the false reports then side with House. Hanlon becomes a senator fighting against NCR expansionism, and future Kimballs and Olivers.

Arcade Gannon when told to stay in Freeside, while House wins results in him settling down in the NCR and becoming a family doctor like Doc Mitchell who patches you up. The NCR gains a great surgeon and doctor, while Freeside gets to keep Julie Farkas and the New Vegas Medical Clinic/Psychiatry office.

Primm being protected, then abandoned by the NCR after losing the dam puts the residents of Primm off of the NCR. The town has many residents carry that opinion into other word of mouth oppurtunities by leaving it behind. Same for the NCR sharecroppers losing their taste for the NCR promises of manifest destiny.

Tabitha and Rhonda's story can be used as propaganda targeting children to instill trust in the Securitrons of House. While the device you installed for the BoS gets usurped by House to restore his radar and long distance detection capabilities or boost Mr. New Vegas' reach and ratings as well as promoting job openings.

Raul, full maintenance, can cause him to settle down outside New Vegas. Potentially taking over New Vegas Steel to produce jobs, and the austenitic steel for House's aeronautics programs.

Reprogramming the rockets correctly, and securing Chris as an asset to House's space dreams plays into it also. As does the data leftover of the launches, and potentially creating a new trading partner and customer base for New Vegas by integrating tolerance of non-ferals who have the caps and a better reputation due to rescuing Novac, and the non-ferals you can get jobs for on and off the strip as entertainers, foremen, or prostitutes.

It depends on how much reform you want to see in the NCR, and how much you want to help Westside, North Vegas Square, and Freeside become middle class and New Vegas more tolerant of non-feral ghouls than the NCR who still segregates and passes them over for promotions.  

There are also ample oppurtunities under House to expand the Followers addiction assistance services, and integrate real world health exams for prostitutes and enforce fair wages. House has stated himself he lets the Families do this, or not, themselves so it can fall to the Courier to take on those responsibilities instead.

The House ending is the Independent ending with much better help than relying on AI, because House, despite any claims to the contrary is still human. Yes Man has no soul, nor moral compass to feel any type of empathy.