Depending on what time you get in you could be potentially sitting in a lot of traffic getting in to the city from Newark. The other option I would suggest checking out would be to take the AirTrain from Newark and catch the Jersey Transit train in to Penn Station. From there it's an easy walk to catch the F at 34th/Herald Square.
Going back to NYC tomorrow!! Guys, please remind me: There are two steps here, right? 1) At the Newark airport, take AirTrain from my terminal to Newark Liberty Airport Station (free), then 2) Take NJ Transit train to NY Penn Station (buy ticket from a machine). (Hotel is very close to Penn Station.) Thanks for any help!
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What you're doing is exactly what I do now. I moved to Florida in late 2015 and still try to get to the city twice a year. I fly into Newark, head for the AirTrain and catch NJ transit at the Liberty station. Only difference is that I buy my NJTransit ticket in the airport. I used to have to switch trains in Secaucus, but last time it just went straight through to Penn.