Sorry, can't remember the websites I used to book my flights and hotel when I went last December, but I can tell you that I flew with Continental to Newark rather than JFK, which was great. It was actually better for us as the bus from Newark (about 30 - 40 minutes) took us to the Port Authority Bus Station which was two blocks from our hotel. The hotel I stayed in was the Milford Plaza, one block from Times Square. I also booked a helicopter flight, tickets for Top of The Rock (the re-opened last year top of the Rockefeller Center) and tickets for a Broadway show on the internet.
We did Macys, The Staten Island Ferry, Wall St (and a quick trip to pay our respects at Ground Zero), helipcopter flight over Manhatten, Greenwich Village, Little Italy, China Town, Central Park, Metropolitan Museum of Art, Empire State (at night), Fifth Avenue Shopping, Grand Central Station, Rockefeller Centre including Top of the Rock. We walked miles but had the most fantastic time! In December the shops are decorated so beautifully and there are ice rinks at the Rockefeller Centre and in Central Park. I'm so jealous, wish I was going back!