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Your best bet is to get back to EWR airport - I assume that the hotel will have a free shuttle - from there take AirTrain to Newark Liberty International Airport Train Station. Then you take either the NJ TRANSIT or Amtrak trains.
I would take the NJ Transit to NY Penn Station - this brings you out very close to Macys etc. Be careful with the names of the stations as they have both got the same names! Penn Station Newark and Penn Station New York!!
What is EWR AIRPORT? WE ARE FLYING INTO newark liberty airpor.
EWR is the code for Newark Airport - in the same way that LHR is the code for London Heathrow......