I know very little about the CUNY program, so this could be completely off base..but sometimes schools will reject you if they feel you're overqualified and know you're using them as a safety school. As an undergrad I got into a few of my top choices but was rejected by other schools quite unexpectedly. Like I said that might not be the case in this specific instance as I'm not really sure what CUNY's program is like (compared to NYU) but it's been known to happen.