The NYC area is a clusterfuck no matter what airport you fly into, but I would suggest Newark, and then take mass transit into Manhattan, as it it would be the least expensive scenario.
A cab from any of the area airports into midtown will cost you at least $100, while a train or a bus from the airport into NYC will probably cost you around $10 each, but once you land in NYC you will still need to catch a cab to your hotel, so maybe another $10 to $25?
My studio is 20 minutes from Newark airport in case you find yourselves stranded.
Send me an email and I'll give you my phone number in case you guys need any help...
support (at) peckerpass.com
You can visit this site for more info too...
http://www.panynj.gov/airtrainnewark...idtownMan.html
Good luck!