NJ transit to LIRR is the absolute fastest method, you can make it in under 2hrs, and no uncertainties of crossing manhattan and then the Van Wyck, the road method could turn into the worst nightmare of your life.

Penn station is the only difficult-ish part of the process, but there are easy to follow signs and plenty of transit staff and passersby to help you out.

Once you arrive at Jamaica it's super easy, LIRR platform is right next to the AirTran, whoever said its quite a walk is obviosly not a fan of walking. I pass through the LIRR platforms daily from the E train to the AirTrain.

You will pay more for a cab ride to JFK than your flight to EWR, and prob miss your flight. Train is the best option, may not be the absolute easiest, but that's why I have strong distaste for EWR and New Jersey in general, it shouldn't be considered a new york are airport, it's in another state.

NJ Transit - NE Corridor train to NY Penn - $12.50 - 30min
Penn to Jamaica - LIRR $13 - 35min
AirTrain to terminal - $5 - 10-15min

Quick tip - remember that njtransit stops at NJ penn before it goes to NY penn, do not get off, NYpenn is the last stop