I’m not as familiar with Septa, but I pieced this together via a quick Google Maps and NJTransit app search:

[based on 12/23 @ 8am departure]:

1. Newark DE to Philly 30th (via Septa Wilmington/Newark Line):

9:04am - 10:12am (1hr, 8min) @ $8.00 fare

2. Philly 30th St to NYPenn (via Septa/NJTransit switching at Trenton):

10:39am - 1:22pm (2hr, 43min): $26.00 fare

I don’t believe there’s a quicker way to get to NYC via train without Amtrak. It depends what you prioritize. The route above is $34 and almost 4.5 hrs (assuming there aren’t any delays between the many stations).

[for comparison: also based on 12/23)

1. Newark DE to NYPenn (via Amtrak 134 Northeast Regional):

4:52pm - 6:58pm (2hrs, 6min): $104.00 fare

Note: only one seat available at this price at the time of writing. Others times are available for $166.

I’m not sure if that helps. But for my money, a direct train is always easiest if that option exists. I can see how the price is significantly higher for Amtrak, but Septa and NJTransit can be very confusing if you’re not familiar and/or switching between multiple stations.

Good luck and safe travels!