I agree 100 percent about the MONH. We still joke that our high-functioning autisitic niece - now an adult - went there when she was small. For ages, she referred to this as the Dead Zoo - which i also heard on a Gallagher special, so maybe someone *told* her to call it that. It is an incredible place for kids - and us BIG kids! - to go to. Not far away is the Frick Museum - a gorgeous mansion full of art - which your kids might not take to. There is is also the Metropolitan Museum of Art - and as long as and your kids skip the endless corridors of fustian portraiture and landscapes, there are tons of things that will thrll them, Arms and Armor. IN the galleries ABOVE that- music instruments (if they are into that). All the Egyptian things. The Temple of Dendur. And my favorite treasure - the Gubbio Studiolo. Designed for Italian nobility, it is a small room decorated ONLY with 12 kinds of naturally colored inlaid wood. If you stand in the right spots, it *appears to have cabinets overflowing with books, stuffed animals, globes, armillaries (globes with circling known planets), etc., etc. , including a fur hat on a bench. But yo soon see that there are NONE of these things - it is all fool-the-eye-perspective work. There is not a whole lot of current CGI that is nearly as stunning as this - and it is almost 500 years old. Done with a good eye, really sharp knife - that's all. Nothing is drawn or painted - all inlaid. The last time I saw inlay work *almost* this fine, was at the huge guitar display at the Musical Instrument Museum in Phoenix. But this additionally PERSPECTIVE work - mind-blowing. There are countless other museums in NYC, but not all are for kids - or even adults, unless they have a serious interest.
I am also originally from MA, and we returned there for grad work at BU. We go back to visit every so often. If you are driving thru the Berkshires, or want to detour, stop in at the Mass MOCA in North Adams. Incredibly interesting HUGE things for everyone to experience - a a really nice brewery our front for Mom and Dad (yes, serves lunch - several places on property do.) YOU might know about this - but *other people also read here, so might poke them to go!
Have a great trip - and come up to explore the Hudson Valley, too! Lotsa cool things up here to see and do - and they you hop on the Thruway, then the Pike . . . before there were self-driving cars, we swore that OUR all could do this for us unassisted.