Bryant Park will have their lovely winter village (opens 10/29 so as long as it is not tomorrow you should be good) - with shops and skating and food - a good way to break up your walk from penn to central park
If it rains, you can go to the Food hall/ shoppes in the Plaza Hotel (lower level.) Lots of good treats and lite meals. It is right off Central Park. Good on sunny days too!
I agree with the above poster about NYPL on 5th Ave, adjacent to Bryant Park. There is an exhibit currently running in which the library has gathered all the artifacts from their collection about that man of the year, decade whatever, Alexander Hamilton. I’ve been to exhibits at NYPL on Friday afternoons but not sure how late the building is open.
The winter village at Bryant Park opens this Saturday, Oct 29. So, if you are coming after that date, it is a nice place to spend some time and maybe find a nice holiday gift to take home or just find a table and people watch. I like to get the hot cider and relax for a little while.
I agree that it might take an hour to get uptown and what about if your connection is late.
If you have the time, you might do something I have only done once, even though I literally work 2 blocks away and pass it every day - go to the top of the Empire State Building at 34th and 5th. I believe that you can pre-order tickets for a set time so that you don’t have to wait on the line.
I have to admit to total unfamiliarity with the Winter Village at Bryant Park. I may take a walk over one day at lunch.
Hate to be a downer, but you may want to have two plans ready: one if your train arrives on time, and Plan B if your train arrives late.
For something very nice but a little different I’d suggest the Morgan Library and Museum. It’s got a very nice collection & exhibits, but small enough that it is do-able in an hour – see http://www.themorgan.org/– the web site says it’s walkable from Penn Station or Grand Central… here’s the map link so you can see where it is: http://www.themorgan.org/visit/directions
(My daughter works in midtown, so when I visit I’ve often looked for things to do until she gets off work that are a little less well known)
Top of the Rock view, MOMA if you like modern art, Central Park Zoo, Central Park itself
I forgot to say Times Square!
@TheGreyKing — oh no! Avoid Times Square, at all costs…pedestrian gridlock.
Seems OP has been to NYC before. And we don’t know how viable some ideas are, with only an hour or so. Some of us are satisfied differently. Eg, calmom’s comment about the Morgan or a quick look inside the NYPL. When I head there next, we plan only 30 minutes in the Metropolitan Museum, but we’ve been there often and only plan to see one new exhibit. Some places, you’d just be getting your bearings or into the elevator at the Rock, in that amount of time.
This may be too late for the OP today, but the Grolier Club is worth a visit; they have rare book and graphic arts exhibits, and entry is free. They are also SE of Central Park.
http://www.grolierclub.org/
@thumper1 had the right question, which train station?
If you are coming into Penn, the advice was also good: (assuming the weather is not awful)
Walk or take the 1 to 42nd street.
Walk through times square. It’s crowded for a reason. If you can go back through TS after the event it’s more impressive when dark.
At 48th Street cut over to 5th Avenue and see the shops, St. Pat’s, Rock Center, and maybe end up with a Manhattan at The Oak Room at the Plaza or the rooftop bar at the Peninsula. Haven’t done top of the rock but I am sure that’s cool too.
There is way more than an hour or two to do between the two locations. You almost can’t go wrong. Just don’t talk to anyone in a costume and don’t eat anywhere that has pictures of the food outside.
Good thing you’ll be walking vs driving, Iglooo! As they say, the only place an hour from midtown…is midtown. 
If you were looking to spend an hour on a Friday night post 6 PM in midtown, the Morgan LIbrary is free or pay what you want… If looking on the Upper West Side, NY Historical Society is pay what you want and MOMA is free on Friday night but huge lines to get in.
Only an hour? Pick a cafe,sit there and people watch. It will probably be very interesting.