I concur with everything the people said (sadly, never having taken a helicopter ride myself). Take Jean's advice and take a boat tour or at least a ferry ride or two. Even 'tourist traps' like South Street Seaport are not to be missed. High on my list for the next visit is USS Interpid and its neighbour, a Concorde.
The best veal I ever had (and I had quite a lot of it) was in Tribeca Grill (celebrity-owned restaurants are not tipically my sort of spot, but local colleagues took us there and I am very glad they did). It was soon after opening; I don't know what it has developed into. Of course, you can't go wrong with numerous delis and their 'hero' sandwitches...
I am nuts for a view from a high vantage point; now this keeps reminding me of Twin Towers... The view was spectacular, doughnuts terrible, crowd most colourful. I often took my breakfast in an Italian fast food in the mall below the Towers (scrambled eggs with pancetta, fantastic cheesecake, coffee, unfortunatelly, entirely non-Italian) watching sharply dressed people hurrrying to their offices, wearing sneakers with dress shoes in a bag or sometimes hanging by laces around their necks.... Sigh, all gone now. The Ground Zero is also high on my next-visit list, with a flower or something....