I'll throw my school out there, Marymount Manhattan College. We don't have an MT "major" we have a minor but combined with your Acting major it would feel like having a major. They have dance class everyday and a voice lesson once a week. There are also other classes like scene into song and fundamentals of musical theatre that you take per semester. Plus we have a showcase, which you need to audition to be in, at the end of your four years. I've seen the MT schedules and they are pretty insane so its definitely a big commitment even though its not a BFA degree or a major.
Pace University in lower Manhattan is only the second school in New York City to have a BFA Musical Theater degree program. They are somewhat new, but from what I hear, they are definitely on the rise.
I'm going to second Pace. I was an Acting BFA, but the MT program is very cool. It's more personal and less machine-like. I think NYU is kind of a machine, and from my experience, very impersonal. Still a good school, I guess it all depends on what you're looking for.