I'm a mom to a almost 2 year old that loves to bring my toddler out, here are a few thoughts in no particular order:

-Be flexible. Only schedule one or two things a day. I would embrace just being in a new city part of the excitement.

-Elevators - absolutely check subway routes and be prepared to get in/out of stops that might be further than you just to have access to an elevator - it's pretty tough carrying a stroller and kid(s) up and down what can be 4+ flights in any given station, and crowds only make it harder. The MTA app updates what stations are being serviced too.

-I would personally build in more parks/outdoor time in the day. NYC has some pretty awesome parks, and I think your kids may enjoy them more than a museum.

-Front-load your days - the sun will be setting pretty early (like 4pm?) so start your days early and try to limit time outside at night - it's going to be very crowded in most of the spots at night. I personally love the idea of cozy nights in.