There are so many things you can do - but you don't have time for everything. get a guide book and pick the things you really want to do and then plan for 1 thing per each half day at the most.
If things are close together, you may be able to squeeze a few extra in, but this does make your time there rushed. Obviously plan to go uptown for the day and do a couple of museums one after the other, or plan to do statue of liberty/Ellis island along with Ground Zero as they're both at the south end of Manhattan.
Depending on when you're going (peak or not), there can be long lines (esp for the museums).
Use the subway to get around quickly, and remember Times Square and The Empire State are open practically all night! almost 7 years ago
HI Zan, NYC is a hot topic on Ask a Nomad. Here's a thread you might find useful:
http://answers.worldnomads.com/questions/united-states/72/what-is-a-must-do-in-manhattan almost 7 years ago