The question is whether the NCR's industrial base is ready for such an aircraft. The Vertibirds were mass produced by the Enclave, yes, but they're manufactured using different techniques and likely have completely different control schemes. The B-29 is old technology, likely with very few copies of the blueprints available. As far as we know, the Boomers' plane is the only 1940s bomber to be in service, and I doubt they'd be willing to let it be dismantled so the NCR could learn all its secrets. And even then, there's only so much they can learn.
Moreover, what would be the point? There's very few clear spaces for such a large plane to land and turn around for takeoffs and refueling/rearming, so it would take a huge effort to clean up enough infrastructure to support a bomber. I doubt they have a lot of air-dropped bombs, so it would be pretty expensive to use the plane for the massive carpet bombing attacks (or nuclear bombings) that it was designed for. And who would you bomb, anyway? The Legion is the only group that can stand up to the NCR in size, and a carpet bombing run is a waste because their settlements are relatively small. The lack of available airfields and landing strips means that it would be very inefficient for transport, since you probably won't have an airfield immediately next to your destination. You'd still need to bring in the trucks and pack brahmin.
The B-29 is a relic of an old age for a good reason: it's just plain not worth it. Even today, strategic bombers like the B-52 are sparingly used because most targets don't require sending in a gigantic airplane to saturate it with explosives. The NCR faces even fewer challenges: their enemies are mostly foot soldiers and raiders who can be killed efficiently with assault rifles and shotguns. Even howitzers like the Boomers have are overkill most of the time. Most of the problems the NCR face can be solved by sending in infantry. Transport is much more flexible if done through trucks and brahmin, since they're not reliant on pre-prepared landing areas.