Awesome trip report! Yes, I always choose the north side of the train but mostly to avoid the glare of the sun. I've been meaning to take a trip from NYP out to the 'Island' on the Long Island trains... hope to do it soon.
For a perfect hotel at NYP always try to get the Fairfield Inn across the street. Always wangle a way with points to stay there for free... but ya need a lot of points!
While there I have no hesitation to get a meal from the Halal trucks... really good and New York is strict with food inspections so it's always been a good choice for me.
RE: North along the Hudson [on the Hudson side of course] is some of the best viewing Amtrak has to offer. Below taken last winter:
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