Depends where you fly from.? But we flew to Newark and stayed that said on the waterfront right oppisite New York.The train station was right next door and took us under the river to Ground Zero if you wanted to .
I've flown into both Newark and JFK. When I flew into Newark I stayed near Times Square and got the bus from Newark into the Port Authority Bus Station, which was just 2 blocks from the hotel I was staying in. If visiting New York for the first time you should really get a good guide book, I recommend A Brits Guide to New York, which tells you about transport (including the airports) and loads of 'Brit tips' - like where to find a public toilet (sorry, rest room).
JFK or newark would be fine. Sounds like Newark is a bit further for travel.. I would choose JFK, though if price difference is worth it go for Newark.