I've been studying freight mobility in Manhattan with my Captstone Team, and I recently started digging into the history of Manhattan's only freight railroad, the West Side Line. Most New Yorkers know what's left of it as the High Line elevated park. The image above shows the west side line extending from just below Canal Street all the way up to the Harlem River.
The railroad used to run right down the street on 10th and 11th avenues, but it was elevated and re-routed through the middle of the blocks as part of Robert Moses' West Side Improvement project. The northern section of the line was covered, and now runs under riverside park. (this is the freedom tunnel that has been studied, written about, and filmed over the years)
The entire section north of 34th street is still in active use for passenger service by Amtrak.
Why can't we bring freight into Manhattan on trains anymore? One reason is the Selkirk Hurdle, the closest rail crossing of the Hudson River. It's located over 140 miles north of the city, and any freight train destined for NYC, Long Island, or any other points east can only cross at that location. It's cheaper to unload in New Jersey and switch to trucks, but our current situation with congestion means that practice isn't sustainable. If the Selkirk Hurdle weren't an issue, what would it take to bring the occasional Freight train into Manhattan?