She should fly into JFK. The AirTrain/subway route will probably be faster. You'd take the E, and get off at the first stop in Manhattan, 53rd and Lex. From there it would be a short walk to 56th and 3rd.

If she flew into EWR, she'd have to take a train into Penn Station, then either switch to the subway or take a cab the rest of the way. More trouble than it's worth in my opinion.