I think a lot of the thought about combining the NE with NY isn't about how great NY is (because it is). Rather, it is about how weak the rest of the NE is. Teams from the NE as a whole don't perform historically great and may seem "less deserving" than a few other possible at-larges out there from other regions. So by combining, if there is a deserving NE school, they will either be in the top 2 and earn it, or get the consideration from being in the top 4.
Some might reply that it would be very tough to break into those top 2 or 4 spots with many good NY teams... California is the same way and leaves home many very good XC programs every year; same with the Midwest; same with the SW; same with almost every region.