Union Square, I remember it well, on the north side, mid-block was the Fitzhugh building, three story high foyer all in marble, four manually operated elevators (with a call person on the main floor) with mesh doors so you could see the floors going by, which were numbered. Medical Building, super high class construction. later the elevators were automated, but still had glass outside doors (you could watch the cables moving while waiting for the elevator--no need for "up" and "down" arrows!).
South East corner was the City of Paris store, and south side was Macy's with Blum's cafeteria. I don't recall the east and west sides of the square, so the St. Francis is quite possible.
I don't remember the C of P having a train on the roof--they did have this magnificent stain-glass skylight over the center arboretum, in which a HUGE Christmas tree was set up every year. I don't believe that roof could have had a train on it; if it was one ON the square, it would have been Macy's, but I remember the one on the Emporium roof. The one one ebay sure looks like it might be that one; but you are relying on a six-year-old's memory! Christmas time in the City was glorious to a young boy! Oh, the toy train departments!! I also remember the elevator announcements: "Bing-Bing Third Floor, Ladies' Foundations"9