I will be bringing 2 13 year old girls to see Rent (matinee) on a Saturday in February. The train gets in at 11:00 and leaves at 8:00 so we have limited time. I am looking for interesting ideas outside of the usual tourist attractions/restaurants but still able to be hit in the time windows I have. This is not their first time in NYC. Any ideas?

Have they been to Dylan's Candy Bar?

Maybe afternoon tea?
http://gonyc.about.com/od/restaurants/tp/tearooms.htm

At that age, they might get a kick out of Madame Tussaud's Wax Museum, especially if they're into celebrities. A discount is available through Season of Savings (seasonofsavings.com)

Assuming your train gets in to Penn Station (not Grand Central), you might have time for a quick trip down to Chinatown/Soho for some shopping.

Let's be realistic about how much time you have--3 hours before the show and 3 hours after the show.
Assuming you'll want to have lunch, that leaves 2 hours before the show. I don't think I'd venture too far afield beforehand. Since they've never been to New York City before, how about a few "typical tourist" atractions, such as Rockefeller Center, St. Patrick's Church, Fifth Avenue, etc. before the show?
Afterwards,sgain, I assume, you'd want something to eat, again leaving you about 2 hours. How about a stop at Top of the Rock at sundown?

Since it's not their first time in NYC, it's hard to know what they've already seen. But w/o that knowledge, agree with the advice you've gotten. Arrive at 11 am. Go to Rockefeller Center. Go to Top of the Rock. I think there's a 2 for 1 discount on seasonofsavings or Paint the Town (go to nycvisit.com for details). Maybe they'd like to skate at Rock. Ctr.? Walk across to St. Patrick's. Maybe they'd like to shop in H & M. Have lunch. Go to theater. Come out and go to Mme Tussaud's.

Do they watch Project Runway? Seeing Parsons is fun. I'm not sure if they do tours, but they might like that.

What and where is Parsons?

Parsons is an art/design school in Chelsea that often has exhibits of student work/designs.
http://www.parsons.edu/

We had about 1.5 hours to kill between eating lunch and our matinee of Wicked last Sunday. I took my son to the Sony WonderLab - you need advance reservations for this. It was a good way to spend an hour.