Thank you all for these great suggestions. The reason for no train is that my father is not a "walker" hence one of the reasons why he is taking us on a cruise instead of a different type of vacation. He most likely won't even be getting off of the ship at any of our stops, for example. We also want a very relaxed trip up and back to the terminal from Philly and we would have to still get from my house which is less than one mile from the Philadelphia County line to our local train stop or uber to 30th Street Station then to Penn Station and then to the Manhattan terminal - too many transfers. And since he is paying for most of the cruise, it's hard to argue with his wishes. So unfortunately as much as I see where people are coming from, we are not going to take the train. No ferry either.
We have ubered straight from my house just over the line Philly line in Montgomery County, Pa to and from Newark airport before (which was less than $200 each way) so I am also going to look into ubering to and from Manhattan as crazy as that sounds.
I'm just testing the waters to see if we can find any way to get up there and back with our criteria that is less than the $1000 the transportation company quoted us. And who knows, all of this research may just make us double down on the transportation company at the end of the day anyway. Too bad we just can't cruise from Philly.
Anyone have any trustworthy long distance transportation company suggestions?
Again, thanks so much for everyone's time and efforts!