Everyone is different. Nobody on here can help you decide! I personally, have always felt that super long commutes destroy quality of life. I have seen examples of this with others and never wanted to put that on my husband. We live in Long Island, he works in Long Island as well, about 1/2 hour away. If your hubby works in Manhattan, I would personally not want to have him commute any more than an hour (DOOR TO DOOR) each way. I say door to door, because you cannot calculate exactly how long the train is as the commute. Count in how far from the train, how far from the train to the office. How is the train schedule, etc.
If it were me, I would take a smaller house, with a smaller property in order to have a shorter commute. Since working is most of what we do, if you have an hour and a half each way door to door commute let's say, then an 8 hour day plus an hour for lunch, your hubby will be gone from the family 11 hours a day. In other words, barely ever seeing the little ones except on weekends. Not my cup of tea for my family.
Make a "pros" and "cons" list of each area.
Also think of other things like proximity to family? Proximity to beaches? Children's activities in the areas like children's museums or zoos or gymnastics or swimming lessons, what kind of libraries they have? What about pediatricians? Any special services your kids need? Your insurance plan and what doctors are available in the area? What about friends in the area?
ALOT to think about!!!