Do NOT rent a car if you are going to Manhattan, unless you absolutely need it to get somewhere in the suburbs or boonies during the course of your trip.
A rental car will cost you $60-100/day for the car, plus $20-50/day for parking, plus gas, plus the associated hassles of having a car in the city.
Public transit:
- LGA = $2 (~60 minutes)
- JFK = $7 (~90 minutes)
- EWR = <$5 (~90 minutes) OR $13 (~45 minutes)
Taxis:
- LGA = ~$25-30 (15-45 minutes, depending on traffic)
- EWR = $50++ (20-60 minutes, depending on traffic)
- JFK = $45++ (30-90 minutes, depending on traffic)
Assuming you'll probably take a taxi, I'd probably go with LGA unless EWR was at least $50 cheaper, in which case it's a toss-up.