Let's be realistic, nobody who lives in suburban, Central NJ (where I grew up) is going to take Amtrak/NJT to LIRR to AirTrain. MAYBE you could convince a solo traveler to take Amtrak/NJT to EWR, though certainly not a whole family.
We almost always flew from EWR, it was a 40 minute drive (PHL was probably 1h). On a few occasions we had to go to JFK (e.g., group trip to Israel; only option was El Al from JFK back then)

In any event, yes, best case at very off hours is that JFK adds maybe 30 minutes (38 minutes to EWR from my childhood home right now per Google Maps, vs. 1h6m to JFK), but it could easily take an additional 30-60 minutes or more.