Just to add to this. I used to live in Central NJ, 2.5 hours each way by train/walking (could have been 1.5 hours by car). I would leave at 5am and get home at 8pm (worked 9-5), to me no way to raise a family (couldn't even have a dog). Did this for 2 years. Moved closer to the city (45 minute door to door bus/walk), but now work 8-6. Usually leave at 7am get home around 7:30pm, on nights I don't go to they gym. Still would like more free time, but the rent increase wouldn't be worth it ($800 for a studio vs $2k studio/1-1.2k w/ roommates).
Growing up in Central NJ, my dad would drive to the city. Usually, we would not see him in the morning. One of the memories that stuck with me, is a day that my mom prepared a nice meal, we were all seated at the table, and my dad comes home to go eat in front of the tv. I understand now, how tired it can be after a long day. But at the time, it left an impression. We had a lot of family support, which was very helpful. Personally, if I were in your position, I would try to stay in the city until the child is out of ~first grade. At that point I would consider moving to the suburbs. It is tough moving schools once friends are developed, but it is a little easier now with technology.
Another thing with the subway/train commute is delays. If they ran on schedule, it would be fine, but they were usually 10-15 minutes late for me. And then you have to consider where in the city. I used to take the train into Penn, but worked near Grand Central. It was the crosstown commute that got to me. The train ride was just over an hour. Perfect amount of time to study certifications/catch up on tv shows, while having my morning coffee...but I tried walking/subway/citibike and it was too much of a time suck.