I echo alot of what has been said here, I go to NYC about 4 times a year (getting ready for my after Easter trip in May, I'm a church musician, I do a trip after Xmas and Easter as a gift to myself). To make the Trainworld trip better, get back on the F after you visit, take it the rest of the way to Coney Island, you'll see the Coney Island yard, one of the largest train yards and it's a subway yard! The station itself is very impressive Then take another line back in, the B and D line go over the Manhattan Bridge. Yes there's also trainland in LI, (Long Beach Branch to Lynbrook) and there's also Nassau trains, (Babylon branch to Freeport). Neither are terribly far from Manhattan, The stores will probably be closed Turkey day, so either get that in before or after. There's also the transit museum in Brooklyn accessible by a few different lines, not sure if that will be open (probably, but not on the day itself). They also have an annex in GC, which I think will have a Lionel display up and running by then.
I would also highly recommend Grand Central, Jerry said it was the "St. Patrick's Cathedral of trains" and as an organist and Catholic I would say that's right on. If you like seafood, I highly recommend the Oyster Bar. If you want to actually take a train from there, you could take a Harlem Line train to the Botanical Gardens if their display is up and running, the Hudson line has beautiful views of the Hudson (sit on the left side of the train in the direction of travel, you could go to Croton-Harmon, there's a LIRR yard there), and the New Haven Line is good if you want to see what the Northern part of the Northeast Corridor looks like (Amtrak joins up with MN at New Rochelle).
If you want to see the real Hellgate Bridge, take the N/Q all the way to the end of the line to Astoria-Ditmars, it literally stops right under it (I always know I'm in NYC when I see it from Amtrak), you can use an Amtrak schedule and call for statuses if you want to take pictures.
Now while yes I concede Penn station is certainly not GC (although I didn't grow up with the old one, and for me while the new one is nothing to speak of architecturally, there is a certain "train energy" that I like in there), there is one gem: Tracks, it's a small restaurant on the LIRR concourse, right near the LIRR ticket windows. There's a bar infront, but a more quiet dining room in the back. Trains everywhere: models, placemats, photos, and the menu is small but tasty and not badly priced (for NYC at least). If you exit out the back door to the Hilton passageway, you'll see an old sign that says "PENNA RR" with an arrow.
I would encourage you to book the train as early as possible. If you don't know, thanksgiving week is Amtrak's busiest travel time (the commuter railroads will also probably run extra trains, if you wanna see America taking trains, this is the week) so book early. I would assume the same for hotels. If you wanna like watch the parade from the hotel that's one thing, but if you're more flexible, in Jersey City in NJ. 25 min ride to 33rd street on the Path train, right near Macy's. That's another thing, you can take the PATH to Hoboken, lovely station. I say, if you're into passenger trains, NYC is paradise.
], real trains, and the GCT museum display and layout. Then circle back to Sacks 5th ave, St. Patricks, and Rockerfeller center [all in the same area] BTW- I would place GCT above Reading terminal market becasue it not only has the food BUT Real and model trains as well!
