Rooms are a little bit bigger at the New York and it's a closer walk to the parks. I also understand (though I haven't been myself) that breakfast can be less f a "bun fight" as the hotel has about half the number of rooms of the Newport Bay. The flip side to this, is that you can't do the Good Morning Fantasyland Breakfast if you're staying at the New York - so if they continue this perk and you really want to do it, then the Newport Bay is your choice.
Apart from that it could just depend which decor you prefer!!