Walk west to Lexington Avenue and north to 53rd Street, and take the Downtown E train (of the A-C-E, the blue line) from Lexington Avenue-53rd Street to 34th Street-Penn Station.
No, the AirTrain takes you to and from the subway, and the subway takes you to and from Penn Station. Take the AirTrain to the Howard Beach Station, and get the Manhattan-bound A train (of the A-C-E, the blue line) to 34th Street-Penn Station.
No, but it does stop at penn station and you can take the subway
Take the Uptown E train (of the A-C-E, the blue line) from 34th Street-Penn Station to Court Square.
You don't need to take the subway to get from Penn Station to 28th Street and 8th Avenue (which is in the Chelsea neighborhood, by the way, not in Greenwich Village or Greenwich Connecticut). Penn Station is at 34th Street between 8th and 7th Avenues. So you can just walk there.
You don't have to take the subway; it's 2 blocks. Penn Station is at 34th Street between 8th and 7th Avenues, and 520 8th Avenue is between 36th and 37th Streets.
Take the Uptown 1-2-3 (the red line) from 34th Street-Penn Station to 42nd Street-Times Square, and transfer there to the N.
MetroNorth from Poughkeepsie goes to Grand Central. Amtrak from Poughkeepsie goes to Penn STation. It's very easy to take MetroNOrth to Grand Central and then get the subway to Penn Station.
Take the Downtown 2 or 3 trains (of the 1-2-3, the red line) from 34th Street-Penn Station to Wall Street (at William Street).
3 uptown, transfer to S, then 6.
Take the subway to 34th St (Manhattan). That's Penn Station. Take Amtrak.
The 1, 2, and 3 trains go from Times Square to Penn Station. The A, C, and E trains run parallel, going from Port Authority to Penn Station. However, the Port Authority Station and the Times Square Station are connected underground.
Penn Station is at 34th Street so it is 20 blocks away from 54th St. You would take the subway two stops north.