Maybe I missed which suburb you are in.
IF you can avoid Rt 1 [slow] and instead take the Penn Turnpike to NJ Turnpike is a good gamble as you are going mostly against traffic and can make it to EWR airport in almost very little time. From there AirTran directly to NJ Transit and into NYC within 25 minutes (midtown).
All rental agencies are represented at airport and your only unknown (which you can ask the NYC forum) how best to buy gas before returning to rental agency. The gas station at EWR is about $1 p/gallon higher vs. surrounding gas stations.