I can highly recommend this place,
http://www.chelsealodge.com/
not in the centre of New York, but Chelsea is a really cool area and 10 minutes on the Subway will get you into the centre. BTW, I dunno if you have been before but Manhattan is a hell of a lot smaller than you think. And we arrived in the worst blizzard for years when we went there in December so bring some warm clothes
You can buy your Empire State tickets online, so while you will have to queue to get up there, you can beat the queue to buy tickets.
It's funny, but New Yorker's have a reputation for being unfriendly, but we had a warm welcome wherever we went and found them really friendly and helpful.
Also worth a visit....
http://www.bubbys.com/ for Breakfast
http://www.intrepidmuseum.org
http://www.rioc.com/
http://www.c21stores.com for Shopping (it's actually at Ground Zero)
http://www.myriadrestaurantgroup.com/tribecagrill/index.html for dinner
We did go to Ground Zero and it's wierd, looks like a big building site, then you look around and see the burnt out buildings around it, and pictures of the dead placed on the fences... then it starts to hit you what happened that day, was a very moving experience.
Our photos at
http://groups.msn.com/TheWonderfulWorldOfLooPoo/usa2003.msnw?Page=1
Jonathan