While understandably inconvenient, what you describe is technically correct. NYC is really New York City (LGA/JFK), and EWR is really just Newark.

In the past, I know that CO had it programmed such that NYC was Newark City (EWR/LGA/JFK). And given how much effort CO puts into marketing Newark as New York by displaying things like New York/Newark on departure boards, this is probably a mistake by the CO web folks down in New York/Houston.