Newark AirTrain is off at the moment I think (we were there a few weeks ago and it said it was closing May – July for maintenence).
Airport Express bus is quick and good – runs from Grand Central, Bryant Park and West 41st St under the Port Authority terminal so if you’re staying in Midtown it’s ideal. When we got it we were the only people on it and was $16 each, single.
Taxis from Manhattan to Newark are expensive as they cross a state line (New York/ New Jersey) – $70 plus tip and tolls so you’re looking at close to $100, we were told – the concierge in the hotel told us to get the bus.
(The fixed fare is JFK as that is still New York State.)