We had a few days with our 4 in Sept 06. Kids were 10,8,5 and 4. We did Empire State - security was very tight when we went, lots of bag checks, kids told they weren't allowed to sit down when queuing for ages ("it's a security risk m'am" ), and another ticking off for sitting on the wall at the top to give the younger ones a better view!
Enjoyed the bus tour in the rain - guides do often remind you to tip them.
Caught ferry to Staten Island and got good view of Statue of Liberty, then came straight back! Think it was free or very cheap!
Kids loved the freedom of Central Park and a break from the hustle and bustle.
We stopped off at Ground Zero on the bus trip - thought the older kids should see it and understand what happened. Very quiet and eerie feeling with some amazing photos. Glad we went but guess it wouldn't suit all. Not sure what stage its at now though in terms of redevelopment.
Did Coney Island - pretty tacky but kids enjoyed the rides. Had hotdogs on the beach from Nathan's World famous(?!) hot dog stand!
Metro system efficient and felt safe in the areas we went to but didn't use at night. Kids very excited going in yellow taxi (small pleasures ).
Dave and Busters was pretty child friendly places to eat at (sorry, can't remember where it is!) but annoyed at having 15% service charge added as we were a large party (family of 6 )?!
Hope this is of some help and you have a great time.