For weekday travel, starting from Penn Station, EWR can be slightly faster than JFK if traveling by rail. But on weekends when there is more frequent LIRR service from Penn to Jamaica than there is NJ Transit service from Penn to EWR Airport Rail Station, JFK can be a faster trip.
From the Financial District, PATH from WTC to Newark Penn Station, followed by the Q62 bus to the airport can be a fast -- and economical -- option.