since you want to finish your day at Penn Station, I'd start downtown, by taking the E as Spago suggested. try to be at the front of the train -- the WTC stop is the last stop on the E (the A and the C, which also run on the 8th avenue line, continue on down to Fulton Street and go to Brooklyn). they've set up a memorial wall and viewing area at Ground Zero, and you can still see the display of memorials left on the fence at St. Paul's Church. I'd also walk down Broadway to Battery Park -- a short walk, past Wall Street and Trinity Church -- to see the sculpture that used to sit on the WTC Plaza but now is at the entrance to the park. if you walk down to the water, you can see the Statue of Liberty sitting in the Harbor. if you walk to the other end of the park, you can take a ride on the Staen Island Ferry -- it's free, and it takes you right past the Statue.
then I'd walk walk back up Broadway a few blocks, turn left onto Recotr and walk to the corner of Rector and Church to catch the subway. take the N or the R to 34th, and change trains -- the B, D and F go right to Rockefeller Center. you can see the tree and look at the windows in Sachs, and if you walk uptown towards Central Park you'll walk past FAO Schwartz and the huge
Disney Store and the Plaza Hotel. if you'd like a nice lunch I'd recommend Ellen's Stardust diner on 51st and Broadway, or (if the lines aren't too long) go across the street to Mars 2112. or I'd walk down Broadway towards Times Square -- there's a Planet Hollywood. or if you just want McDonald's, go to the one on 42nd Street near Madame Tussaud's wax musuem. if you have the time, the museum's a bit pricy but lots of fun.
since you're going to be at Penn Station anyhow, you should take a look a Macy's windows. they do theme windows on the 34th street and Herald's Square sides of the building. if you have the time go up to Santaland -- I think that's the 8th floor.