Just thought I'd jump in and tell you that I live in NYC and would be glad to answer any questions you might have. Just send me a PM.
As for some of the advice given here, it's pretty good. Here are some of my thoughts:
Central Park - don't spend hours. Perhaps an hour at most to stroll around. It's huge and there's really not that much to do in terms of "touristy" stuff. The zoo is a good choice given that you have a 5 year old, but keep in mind it's pretty darn small. Here's a bit of trivia. For years after Manhattan was settled, the park was actually where farmers lived and kept livestock, grew plants/vegetables. Keep that in mind as you stroll about. It boggles my mind to think that I'm walking on old farm in the middle of NYC.
Whatever you do, don't take the double decker bus! It costs a HUGE amount and a number of the guides....ummmm... how do I say this delicately? LIE THROUGH THEIR TEETH! One of my friends used to work for the touring company and in order to keep the patter going, they just start throwing goofy "details" thinking that out of towners have no clue. I've often wanted to get on a bus and scream out, "LIES! ALL LIES!" and run like the wind. Take the subway. It's super fast, really cheap and pretty convenient. If you're nervous about it, I can always tell you what lines to take at what stops, etc...
As for NJ vs. a NYC hotel, I totally agree. If you can afford it, stay IN Manhattan. During the hours that you'll be coming in to the city and heading back to your hotel, you likely will be stuck in rush hour traffic. It's a holy nightmare and takes foreeeeeevvvvvveeeeerrrrr. The Westin is decent and convenient.
As for your overall itinerary, here's what I suggest in order of how you should do it:
Museum of Natural History - neat place, I love it. Might be a bit boring for your 5 year old but you'd know better than I. It's my favorite museum.
Central Park & zoo
FAO Schwartz (just thought I'd throw it in because it's a kids mecca)
American Girl - hell on earth for me. I'd rather stick rusty sharped spoons in my ears than walk in here but little girls and not a few older women folk think this joint is nirvana. Sticking a hot needle in an old silver filling is fun for some too, but I aint gonna do it. Go figure.
World of Disney - this is the DIS
St. Pat's Cathedral
Rockefeller Center/Top of the Rock
Times Square - check out the Toys R Us with the indoor ferris wheel, a lifesize animatronic T Rex and a walk through Barbie's Dreamhouse. I like two of those things mentioned, the other is just kind of trippy. I won't say which.
Then you hop on the subway and head down to Little Italy and grab some pizza at Lombardi's. Then stroll around the neighborhood and head into Chinatown. I hate Chinatown but tourists tend to like to stroll about and see the sites, buy knock off designer hand bags and wonder what the fishy smell is.
FYI, I prefer Lombardi's. Best in Manhattan. The other half always shouts me down and agrees with others here that John's Brick Oven in Greenwich Village is better. He's wrong, I'm right.
Anyway, just PM me if you have any questions.
) But really think about whether, as a tourist, you want to be above or below ground.
