Suggestion for routes to ride?

A friend and I are visiting New York City for a short time this summer during the middle of the night while changing Amtrak trains. We have a few hours to kill and would love to get some more trackage under my belt. What would you guys suggest I ride. Bear in mind we don't mind the darkness outside as it's nothing not the sites outside that we care about, it's the ride .
Thanks in advance for your help.

Since you'll be starting from Penn Station anyway, take the 1 train uptown. You'll get to pass through 125th Street (it's outdoors) and then see (in my opinion) the nicest station (181 St I think) in the entire system. Have a nice time!

Don't miss the IRT Flushing (7) line.

The best elevated run in Queens, IMO.

Well, I may be biased towards my favorite line, but I would walk one block from Penn Station to 34th/6th Av., and get on the "F" train, ride it to Jackson Heights/Roosevelt Av. (One of the greatest lines; you pass through the newest part of the NYC subway from Lex. Av-Roosevelt Island-Queensbridge, three of the nicest and deepest stations on the subway, followed by an amazing express run). Switch there for the famous "7" flushing elevated train. (Great Elevated run) back to Times Sq. Then catch the train of your choice back to NY Penn.

Matt, thanks! That's something I never considered.
Arrow, I rode that route once before but I might consider it thanks to you advice. I didn't notice that station the first time.
Vlissengen, I will have to retake that route. I didn't get to ride the best part of the el when I was there over a year ago(only from Main Street to QBP ridden).

Well, if you can fit it in to your schedule do one of the following lines:

Brighton Beach Line (B/Q), for it's interesting mix of four different modes of railroad travel -- subway, open cut, embankment, and elevated. The embankment run, particularly, when done on the B Express -- gives a claasic railroad look to the operation and dates back to when the Brighton was an independent steam-powered railway.

The 8th Avenue Express (A), is a treat if you get a Far Rockaway bound train. After Rockway Blvd. the line takes on a rustic look as you pass fishing communities and small man-made islands on your way to Mott Ave. The line was originally a LIRR service, and you get that feeling when the train is flying between Howard Beach and Broad Channel....kewl

Not to mention the 6 terminal at brooklyn bridge. You can see the old city hall station

You said you have a limited amount of time, so
- Agree with taking the #1 uptown. Get off at 168th & switch to A train downtown,
- At 145th switch to B/D to Yankee Stadium,
- Switch to #4 downtown & get off at Grand Central,
- Take the Shuttle to Times Square.

From here you can either walk back to Penn Stn or take A/C 8th Ave back there.

The other option is to take the 7th Ave express downtown, it's a nice ride.