Could you be more specific on destinations that you will be flying to (ORD, DFW, IAD, etc.) And what NYC airport works best for you. And are you looking for frequency of flights, ability to upgrade, premium cabin experience, etc.

Many business travelers from the New Jersey area like CO as EWR is a hub and it is the only airline to still offer free ammendities in Coach. Others like Jet Blue (which flies from JFK to both AUS and ORD) but others loathe no F and a poor FF program (such as myself). Others AA as it is fairly generous with upgrades once you reach PLT level and above. AA has major hubs at ORD and DFW so that may work for desire for frequency of flights to those destinations.