The Queens Zoo was surprisingly not crowded when we went there one Chol Hamoed, but it was a few years ago so it might have changed.
Also most beaches (avoid Coney Island) won’t be crowded, so if we get warm weather the kids can play in the sand. Dress warmly because it will be windy. Definitely not for swimming this time of year, but perhaps you can dip your toes. Find one with a playground to maximize the fun and enjoy the view. However, no swimming means no life-guards, so be on guard.
There’s also some Nature center we went to in CT but I can’t find it now. Wasn’t very interesting but “cute” and we had the place to ourselves because it was a rainy day, although they did have some indoor stuff.
Generally, the smaller and more boring the place is, the more likely that it won’t be crowded if it’s out of town (in this case 30 minutes or more from the 5 boroughs, Lakewood and Monsey).