We don't want to be too harried, but do want to see stuff. Does this itinerary sound like a good balance?

11:30 Thurs arrive JFK
drop luggage at hotel near WTC
lunch on Stone Street, probably Adrienne's or Water and Wall
4:15 kids' tour of UN
light dinner with lovely setting at Rare View in Fashion 26 or Grill/pool bar at Hotel Americano (both have been emailed to inquire re: policy for children. Menus at both look good. Met rooftop is closed then.)

Friday
pick up breakfast and snack food at Essex Market
Tour at Tenement Museum, deli lunch
Tour of the Fed
Indian museum if there's time
Chinatown with a friend who knows her way around

Saturday
Breakfast at Russ and Daughters or from Essex St. Mkt.
Brooklyn Botanical Garden with friend who lives nearby, eat Mediterranean on Atlantic Ave (she isn't familiar with those places, has twin kindergarteners--any suggestions?)
1:00 class at Sony Wonder Lab
hang out in Central Park
***need to figure out food here***
5:30 Night at the Museum (AMNH)

Sunday
9:00 am leave AMNH
10-12 brunch on cruise around Manhattan, from/to Chelsea Piers http://www.zerve.com/SailNYC/ArManBru
Math Museum
4:20 depart JFK

It would help to know the make-up and ages of the group. Obviously you have kids but how old are they and what are their interests.

I have heard that SONY is very outdated.

I would not eat on a boat - any boat.

Have no clue what the math museum is.

Depending on the kids they might prefer the Intrepid, the Staten Island ferry, the Top of the Rock (everyone would love this).

You haven;t given yourself much time to get to the city and drop your luggage, esp if you have to wait for checked luggage. And if your flight leaves JFK at 4:20 you will want to be there at 2:20 - unless it is international - so leave the city by 1:20 or so.

1 10-yr-old and 1 mom

Interesting comment on Sony.

Brunch is already booked.

http://momath.org/

No, we won't be checking luggage--we are only there for 3 nights! 2 hrs advance for a domestic flight?????

I've heard (from another commenter on this site) that ToR is very touristy/trying to sell things. That's why I thought a nice rooftop dinner might be a better alternative.

Thanks for your comments. You've given me some things to think about.

Thursday has you all over the city. Doable, but allow time and expect to be tired. By Taxis? Buses and trains? Long walks?

Sunday is a little tight, in my opinion. Leaving AMNH (how lucky to snag the night at the Museum!) at 9 to get to a cruise that starts at 10 would be rushed to me. You usually have to be onboard earlier

JFK does require more time that usual for check in, I'd say 90 minutes before flight is not too much. From where are you leaving to go to the airport and how are you traveling there?
Even if you have only carry on luggage, you may not be able to take it to the museum. You'd still have a limited time at the museum anyway.

nytraveler, MoMATH has been around for months and it has been pretty popular. They also run a lecture series for adults that's been pretty impressive.

"Thursday has you all over the city. Doable, but allow time and expect to be tired. By Taxis? Buses and trains? Long walks?"

Excellent question! What do you suggest? That's the only day of the week the UN does tours for kids, and our hotel and flight are also set, so we don't have much choice about all the running around. (We could run less if we didn't drop our stuff at the hotel, but then we'd be lugging luggage all afternoon).

I was thinking we'd get Metro cards and use the subway. Will that work, or would you suggest something else?

I booked the night at the museum months ago, am surprised to see their website makes it look like there are still openings this month. Anyway, we're looking forward to it, especially since we watched that movie last weekend.

Sunday we will have all of our things with us when we leave the museum and will take them on the boat and to MoMath, so we can go straight from there to the airport. Yes, we'll be lugging luggage, but I don't see any other way to do it. What's the best way to move around town between all those places with it?

FWIW, the "luggage" will consist of 1 wheelie suitcase that fits in the overhead compartment, 1 kids bookbag/backpack, and maybe a briefcase-sized "personal item" for mom, so not *that* unmanageable.

I would check with the brunch boat that they will allow you to bring your luggage aboard. NYC has increased security measures everywhere and many popular venues put restrictions on baggage.

"hotel near WTC" can mean many things, with access to different subway lines. For us to offer the best transportation advice, can you share your actual hotel? Also wondering about the hotel because the Essex Market is not that close to the WTC, so it would be a long way to go to get breakfast.

"I've heard (from another commenter on this site) that ToR is very touristy/trying to sell things."
In my opinion this is a very weird generalization to make about Top of the Rock. As you enter, they offer to take a kitschy photo of your group that you can purchase later. You can walk right by this with no hard sell. They have a gift shop at the top and at the bottom as you exit. In at least half a dozen visits, no one has ever tried to sell me anything aside from asking about the photo.

On the other hand, in my opinion TOTR is the best rooftop view in Manhattan and very easy to do without waiting in a lot of long lines and without having to spend too much time. My nine-year-old nephew loved it.

One option for your dinner with a view is located near the UN -- the top of the Beekman Tower Hotel which is nearby.
http://www.thebeekmanhotel.com/dining/

There were many very long lines for TOTR Memorial Day weekend. Book same day tickets online to avoid at least one of the lines. They were actually telling people in line to use their phones to book.

saacnmama ,the Thursday places are just far enough to make walking a hike, but because subways generally go north south but not east west, you may still have to do a few longish walks or use buses too .Metrocards are good for both buses and subways. You may also want to use a few taxis to take some of the tiring factor out of your days, but since they will be traveling through slow midtown traffic they may take longer than you think and add up on cost . Use Google maps or similar to plot them out, Google Maps and Hopstop can also give best transit suggestions for each leg of the trip

A general suggestion, would you consider eating in places that aren't as out of the way for your other stops? There are restauarnts, diners, cafes at all levels all over the city, so with rare exceptions (those usually being the highest end restaurants), it really doesn't seem practical to go 20 or even 10 blocks out of the way for a casual breakfast or lunch. If you ask (on another thread, perhaps) for specific suggestions like Pizza near the UN, or breakfast near the WTC. people will give some good ideas and you'll save time and a lot of running around.

Sunday we will have all of our things with us when we leave the museum and will take them on the boat and to MoMath, so we can go straight from there to the airport. Yes, we'll be lugging luggage, but I don't see any other way to do it. What's the best way to move around town between all those places with it?
Taxis are certainly easiest, but again, plot out the locations so you'll see that subways won't really work door to door.

BTW your luggage does sound minimal, but it's best to check if you can bring even small suitcases and such on the cruise and to the Math Museum. Some places just don't take bags, and since your hotel is not near any of your stops that day nor on the way to the airport, you can't leave stuff there.