My last 2 trips to NY have been with Continental. Check seatguru.com for seat pitch and guides depending on aircraft (they say 31 or 32"). Aer Lingus's seat pitch for economy is also 32" (they are not included on setguru but are on airlinequality.com). I'm 6' tall and so am never particularly comfortable on flights but have certainly not noticed a difference between space on continental and Aer Lingus. I found the transfer to Manhatten very easy and fast from Newark - you buy a ticket to NY Penn station in the airport, get the free airport train to Newark Airport Railway station, transfer there and it's about 20 mins on train to Penn Station in Manhatten. Cost is 14 dollars each way.
I like the personal video screens on continental, and the chance to watch CSI or House back to back episodes rather than the movie too!