Getting either LGA or JFK shouldn't be a problem. Most of the junior guys that were assigned NY have already bid out to various other bases, so they will continue to have slots for new hires in New York. As someone else said, most of the FO's on the CRJ have been with the company for less than a year and a half. A lot of the EMJ FO's have been there much longer, and a lot of them are getting awarded Captain at this point. Even if you were to get either base in NY on the EMJ, expect to be on reserve for a minimum of 6 months to a year. LGA and JFK EMJ are small bases.
With that being said, if you are single and can move. I'd take SJU ATR and move down to Puerto Rico for a year. It's fun flying. On your days off you can chase Puerto Rican Women and drink rum on the beach. After that you can transfer to either jet, and make 2nd year jet pay.