There have been objections about using the right of way for rapid transit. The old New York Central Port Morris Branch in the Bronx is the only portion that is currently unused. The Hell Gate Bridge is used by freight and Amtrak trains. The rest of the way is occupied by the New York Connecting Railroad and the Bay Ridge Branch of the Long Island Railroad, freight railroads that see a significant amount of traffic. If the Cross-Harbor Freight Tunnel is ever built, it will connect to these lines.
From the Brooklyn Army Terminal to New Utrecht Avenue the right-of-way is very wide, with plenty of room for two new subway tracks next to the existing tracks for the N train and the Bay Ridge freight line. The Hell Gate Bridge can fit all the Amtrak and freight traffic onto two tracks, and has a third track and room for a fourth. The crunch would be from New Utrecht Avenue in Brooklyn to 50th Street in Queens, where there is one track in use, but the right of way only has room for one more.
In 2008 I found that the Draft Environmental Impact Statement forecast 24-64 trains per day using these lines, for an average of 1-3 trains per hour. If the line is restored to two-track service, that would allow plenty of time for commuter trains, or even more frequent service if the freight trains are only run late at night.
Another option is to tunnel under the existing right-of-way in the two-track section and run freight trains underground and passenger trains on the upper level. This would be expensive, but not as expensive as building a new subway.
I also suggested that it might be easier to extend existing subway lines along the right-of-way, thus providing a one-seat ride to neighborhoods closer in, than to run a single train the whole way. So for example, you could extend the B train across the Hell Gate Bridge to Woodside; extend the M train, either from Middle Village or from Jackson Heights, north to the Bronx or south to East New York; extend the L train west to Brooklyn College, or extend the G train south and west to the Brooklyn Army Terminal. I created this fantasy map showing the route that the G would take and some possible stations.
I was inspired in part to write this because of the recent post on Scouting NY showing the inside of the Terminal itself. There are offices now where the warehouses used to be, but Building B still has the tracks in the middle, waiting for a G train to glide in.
The G train arrives in the Brooklyn Army Terminal, with a little help from Pro-Zak and bitchcakesny.
You could even use the skycrane to lift commuters up to their offices. Door-to-door service!