Since NY/Newark is a hub for CO, I think it is your best choice if your travels take you to NYC first and then to Europe. Newark is far easier to commute from/to then JFK if your ultimate destination is Manhattan, especially during rush hour (take the train from the aiport to Penn Station).

Domestically, CO also offers you free upgrades (no miles or stickers) if you are an elite and there is space available. Usually first come first served based on elite status.

Finally, CO offers the largest number of non-stop flights to Europe out of the greater NY area. You can fly from Newark to London, Paris, Rome or any of 20 other destinations non-stop. The only downside is complementary international upgrades never occur even as a top tier elite (i.e. like UA's systemwide upgrade certs). You can always upgrade using miles, but eligible fares are restricted.

Disclosure: I have previously earned CO Platinum, UA premier executive and currently hold AA Gold. My traveling days have been quite reduced since I moved west.