When I went my friend and I did:
Day we arrived - Macys and Times Square
Day 1 Staten Island Ferry, Wall Street, Ground zero, helicopter flight, Greenwich Village, Little Italy, China Town
Day 2 Central Park, Metropolitan Museum of Art, Empire State (at night)
Day 3 Shopping on 5th Ave, Grand Central Station, St Patricks Cathedral, a show on Broadway
Last day Rockefeller Center and a trip up to Top Of The Rock (the top of the Rockefeller Center) from which you get the best views of the Empire State.
I then went again last year and this time, though I did some of the same things I also: walked across the Brooklyn Bridge; went into the lobby of the Chrysler Building; visited the the Natural History Museum (the one that features in Night At The Museum) and had Sunday brunch in the revolving restaurant in Times Square.
There's nothing like getting a good guide book (I recommend A Brits Guide To New York) and making up your own itinery. Have a fantastic time.