Hi Dave,
I went there with the wife for a long weekend for our twentith wedding anniversary.
I guess you have booked flights and hotel but if not check out the Metro Hotel, which was just round the corner from the Empire State Building, has a roof top bar, is only about 10 stories.(was rated as punching above its weight star wise when we went)
You also got breakfast included which a lot of New york hotels dont giive you.
We booked through british airways as a flight and hotel package
you can walk from ground zero to times square in a couple of hours
make a google map and put pins in the places you want to visit, that helps find a hotel (if not done already, if you have it will still help)
go into newark, less busy than jfk
do the empire state building early in the day, less busy
would recommend the city bus tours early in your stay as it then gives you an idea of where things are
bloomindales and fifth avenue for shops
go vist grand central station,
chrysler building you can no go up it as it is a working offic / apparment block but the 30's architecture is great (and it is an in and out visit so wont bore the kids)
if you hotel is within striking distance of a train station get the train from the airport as the roads do get packed, not good on a ticking meter and the fair was cheap
see times square at night, it is busy 24/7
i will try and dig out the other stuff i had, i would definatly like to go back.....