On Wednesday, the ship and crew headed for Naval Station Mayport in Florida.
The USS New York is one of the Navy's newer ships - the front of the ship was built with steel from the Twin Towers brought down in 2001.
Eventually, two more Norfolk-based ships will be moving homeports to Mayport as well.
Next year, the USS Iwo Jima and Fort McHenry are set to make the move as part of the Navy's strategic dispersal plan.
"A lot of it is making sure we do maintain two strategic home ports on the atlantic coast, which really is important... not putting all your eggs in one basket," said Commanding Officer Jon Kreitz.
Mayport was supposed to be upgraded to a nuclear home port. That would mean a carrier would be moved from Norfolk to there, but it was delayed with budget cuts.
Now, the arrival of the New York's almost 330 sailors will be the first growth the base has seen in about nine years.