Take AirTrain to Newark Airport Train Station.
At Newark Airport Train Station, take a NJ TRANSIT or Amtrak train to New York Penn Station.
It takes less than 1 hour and is great if you are arriving at a time when there is likely to be traffic heading through the Lincoln Tunnel (which is unpredictable, but almost always backed-up midweek at 8:00am-10am and 4:30pm-6:30pm).
Fare is about $14 and is probably the best and most economical way to get to NYC from EWR.
You can then take the A train from Penn Station.It is only 4 stops and will take about 15 minutes.
Bus- there is a large coach bus that travels from Newark to either Port Authority, or Penn Station; Fare is $14/each way ($23/RT) and buses depart every 10-15 minutes
Here is the link to the bus service that will take you to Port Authority,(slightly better than Penn Station)
Taxi- travel time can vary widely depending upon traffic… 1 hour is a good guestimate, but can be as quick as 45 minutes or as long as 1 1/2+ hours! Rates are fixed depending upon destination. Base rate for one stop is $56+ $6 toll . There is also a $1 charge for each oversized bag.
Supershuttle This may be OK if you are landing at LaGuardia.Otherwise do not choose this option.By the time you get here it will be time to turn around and go back home.