New York is written as being the hometown of Raynor Zeraph. Interestingly, it was Raynor himself who heralded its destruction. The Battle Royale ends with an army of unexplained Glumlings trampling the town to ruins. (BR:3:17)
Apparently, the city (before being destroyed) contained the Dragon somehow, for it was from its ruins that the Dragon arose in the beginning of the Epic Quest (EQ:1:1) At this point, enough time had passed for the area to revert to grasslands (or, at least, terrain covered the ruins).
Guitar Hero had also apparently dwelt in the underground ruins for this duration of time.
After the Cataclysm, there were two cities with the name of "Neo-New York" built: one in America (the birthplace of Raynor Zeraph, and one built in Epicia (referred to as "Epician New York"). The Epicians had apparently liked the name found in the Book of Epic, and named their capital city after it (EQ2:1:2). Epician New York also contained the breeding-grounds of the Abominations. Raynor actually ordered a large part of it demolished to wipe out the creatures. (EQ2:6:14)
After Raynor absorbed the energy from the bio-weapon (EQ2:6:8) and became the leader of the Abominations (EQ2:6:12), Neo-New York became their headquarters (EQ2:6:14). It is there that he found the Chozo Doorway.
The Epician city fell to the second wave of the Grez invasion (EQ2:11:7).