I've visited the city a dozen times and still don't find the appeal...
I haven't been to the 9/11 memorial, I'll definitely go next time. Ellis Island and the Statue of Liberty are cool if you go when they're open! I've had lousy lucky most times.
I most enjoyed the Empire State Building and Sears Tower; Times Square is hellish but it's mainly THE experience you just have to do! China Town had some awesome food, as did Little Italy.
St. Mary's was beautiful as was Central Park.
Oh and definitely the Museum of Natural History, and the Metropolitan Museum of Art!
Even someone like me who's not a city person, there's something to do! Plenty of pinball opportunities to feed your addiction if you can't escape from it! Or if you have no decent arcades near you. Modern Pinball was cool but it's a bit out of the way!
Enjoy your time in the Big Apple!