Welcome to cruise chat, COREYATMN.
I fly to New York a lot on business and have also cruised from there several times. I'd recommend LGA assuming you can get a good air fare. The taxi fare to/from Manhattan now runs about $45 per taxi. JFK is a few dollars more, but there is a flat fee into Manhattan of about $50, not counting tips.
I don't know where you're flying from, but I also recommend getting there a day early.