We picked up a hire car from Newark back in April. Had the same issue as you trying to do a one way trip and found it was surprisingly difficult to book from central Manhattan to Boston, so ended up booking from Newark. The concierge at the hotel in Manhattan organised a limo for I think about USD50 including tip. It may even have been quite a bit less than that, it certainly wasn't any more. This was for 5 of us and luggage in a stretch. You may notice slightly elderly looking limos hanging around the hotels -usually they have an arrangement with the hotel employees.