... As I recall NYAF last year wasn't all that big. I'm used to big like A-Kon and Otakon, for an example of scale.
Contrast that with NYCC. While I wasn't there personally, by all accounts they took in about 70k last year. So while it's a little unfair, I guess, I totally understand why the con was about 1/4 anime, and 3/4 comics. They're going to play to the majority of their attendees who, in this case, are there for the comics. Likewise, people at comic cons DON'T cosplay as much, so they don't really know how to deal with cosplayers. It's just not as much a part of the culture.
Anyway, I'm not saying it's exactly pleasant, but it is pretty logical when you think about it. And that's ignoring the whole Reeds/Wizard thing going on.