Sounds good...

I would still try to do the 3hr Circle Line Cruise, it goes past Yankee Stadium & also statue of Liberty. Honestly, it's not expensive (from memory around $23 USD) and we found it to be the most relaxing and enjoyable way of seeing some of the big sights. It gives you a really good opportunity to see the NY skyline. It also lets you get up close to the Brooklyn Bridge as you sail under it. Just at least look into it, I thought it sounded a tad boring but my boss insisted I do it (as I'm a travel agent & hard to impress as I've had so many fab travel experiences) but I did it and loved it. The man who does the commentary is absolutely amazing (lots about the history of NY too), I've never seen anyone get so many tips as what this guy got when everyone disembarked.

We had 5 days and it still wasn't enough so if you can get an extra day in then do it. We found that we stumbled across so many things that we wanted to do that were unexpected (like seeing Paul McCartney in the flesh at the big Virgin Mega store in Times Square).

If you want Letterman tickets then don't apply online - we went to the Ed Sullivan Theatre on our first day and registered with the crew. Take your Aussie passports (you need to show ID) if you have AU passports as I think that really helped us win some seats as they saw how far we'd travelled to be there.

Also if you are after an airport shuttle I would recommend NY Airlink over Supershuttle.
Oh - and take plenty of tissues to the WTC site, we went on just an ordinary day and I cried and cried (They had these collages up of paintings that children who had lost loved ones had made 'Miss you Daddy' etc, VERY emotional stuff. I still get tears in my eyes when I look at the photos).

I would still recommend doing Empire State Bldg too.

I don't want to say to take anything off your list because sightseeing is such a personal thing and we all have different opinions. Some people travel and visit every museum going but I like to get out there and soak up just being there and blending in with everyday life (but with the major sights of course).

I am so excited for you, NY is the BEST!!!