The revolving restaurant atop the Marriott offers wonderful views but not-so-great food, and I see that the prices are through the roof (pun intended). They do offer a cheese and dessert menu for under $20 in the lounge which might be more doable for you and your son (assuming that they will allow someone underage into the lounge...perhaps call and check first?).
theviewnyc.com
The Top of the Rock elevator is awesome too and is a great suggestion.
If you head down to SoHo there is a great little store called The Evolution Store. If he likes bugs and creepy things, he will love this.
www.theevolutionstore.com
Also in SoHo, if you have access to Twitter or Facebook, friend/follow Georgetown Cupcake. Every morning they broadcast a 'flavor of the day' that is free to the 1st 100 patrons. If the three of you go in, you'll get 3 free cupcakes, no problem. They are delicious and it's a fun little place to go. Lots of other interesting sites in the SoHo area.
The Intrepid is great. Try to go on a warmer day, if possible. On weekends, you can see the mega cruise ships coming in right next door. Also, this yacht is in town now right near The Intrepid and should be here til April...
http://en.wikipedia.org/wiki/Eclipse_%28yacht%29
There is so much more to do and lots can be done on a budget. Have a great trip!