Some things that might help

Model Railroader/Kalbach's "Building City Scenery for your model railroad" by John Pryke offers a pretty good overview of building structures, putting tracks in the streets, painting and weathering, etc. Pryke's Union Freight railroad, the building of which forms much of the book, is an inspirational urban switching layout (for me, at least). 

A couple of website that might give inspiration and some modelling ideas:

http://members.trainweb.com/bedt/IndustrialLocos.html  An amazingly comprehensive site on small industrial railroads in the New York area.

http://www.nyhrr.com/  A large model railroad depicting the multiple railroads serving west Manhattan.

Karl

Thank you for taking the time

try these sites too

hope these help...as a source of inspiration for your city scenery. i too am returning to

model trains now that i am retired.

http://members.trainweb.com/bedt/indloco/misc.html
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http://www.oldnyc.com/
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http://www.nycsubway.org/wiki/Table_of_Contents_-_www.nycsubway.org

http://www.shorpy.com/image/tid/245
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http://en.wikipedia.org/wiki/Category:Buildings_and_structures_in_New_York_City

i had a source for pictures on the waterfront...darned if i can find it...i may have deleted

the bookmark as i narrowed my focus to passenger service north of the city....but there's

plenty of help here....good luck.

Ron

"combine NYC subway, NYAR local freight, and the CSX"

 What scale and how much room do you have for the layout?  There's a lot of possibilities for modeling that area depending on your space and scale choice..DaveBranum