I could be wrong, but I'm pretty certain that most of the last ten years or so of comic books have mentioned that Metropolis is in the state of New Troy, which is clearly located on the East Coast. (Not being a reader of Batman comic books, I don't know if Gotham is supposed to be in the same state.) L&C definitely went with that since their license plates and police cars all prominently displayed 'New Troy.'
However, I don't believe that it takes the place of New York since Superman has visited NYC--in the comics--a couple times.
If you want a geographical position, you could always just watch the pilot again and pinpoint his location from the map they show when he flies to China for the takeout!
