While there's plenty of information about transportation into Manhattan from EWR vs JFK in the NYC forum, I really wouldn't consider the "crossing state lines" a big issue. Just don't take a taxi to/from EWR, use a car service like Dial7 or Carmel. The price is similar for JFK vs EWR and competitive with a yellow cab from JFK. I think Uber has the "state line" penalty as well, so not a great choice for EWR.