Normally the best way from EWR to NYC is to take the air train to the EWR Rail Station and take the train to Penn. I just found out this won't be true in May, June, or July. The Airtrain is shutting down; How annoying! North Jersey is becoming a transportation nightmare in 2014, with construction on 78, the Pulaski Skyway shutting down, PATH to WTC shutdown on weekends, and other construction projects.
Scott from hackmytrip broke this story here.
Best alternative is probably the bus to midtown available here: http://www.coachusa.com/olympia/ss.newarkairport.asp
However, if the traffic nightmare everyone is predicting comes true, it might make more sense to take a bus or cab to the Newark Path.