Walter,
While everyone's being very encouraging here, I think there may be a lot of tongue-biting going on too.
Never one to fear being labelled a bad-guy or wet-blanket, I'm going to dump some cold water on your plans... not because I want to be a fink, but because I think in the long run you're setting yourself up for frustration.
I see three problems with trying to follow your modelling a section of the water-level route in the space you've got.
1) Space. 4 tracks take up a lot of real-estate.
2) Operations. You're going to be hard-pressed to make all 4 tracks functional, and that relates back to point 1), because all that space could be put (IMHO) to better use.
3) Maintenance. The more you try to shoehorn in the more overlapping levels you're going to have, the more hidden trackage, the more headaches from derailments and repairs.
Now, my reasoning:
Your recollections/images of the water-level route are tied to wide vistas. No matter how you shoe-horn it into your space, you're going to have your mainline in a space you can span with your outstretched arms.
What you'll wind up with is a short section of 4-track with some sort of view block on either end... it'll look like it's in a bowl. It won't remind you of the wide-open 4-track along the Hudson or Mohawk, but it will remind you of how small your layout is.
Trying to make all 4 tracks "live" will eat up so much space that you're going to have nothing but a "slot-car" layout, where the trains just chase around and around. For some people that's all they're looking for, but I think most people with an interest in model railroading find this boring.
What I think you should do is consider looking at other mainline operations of the NYC, like the B&A, for example, or the Auburn Route along the Finger Lakes, or the Massena division heading up to Montreal. You can justify running all your favourite NYC equipment, having a mountainous (or at least hilly) setting with small to medium-sized town scenery.
While it's out of print, try to find a copy of Iain Rice's book "Small, Smart and Practical Track Plans. He has a very good (IMHO) philosophy about model railroad design, and how to implement that effectively in a small space.
I hope you don't think I'm doing this just to drag you down, but I've been down the road of over-ambitious plans for limited space several times, and never finished a layout. I always reached the point where I realized the layouts' limitations and failings before I ever got close to getting it finished, and scrapped it.
From an enjoyment perspective, I've found that simpler is better. I like watching the trains roll, but I like watching them roll through a good setting, with believable scenery, so those are the prejudices I carry around with me. I also like to have my trains behave like real trains - stop in towns and switch industries. I think the best model railroads manage to strike a balance between scenery, running and operation.