Check out the official website:http://www.imax.com/magnificentdesolation/
In the "About the Film" section you can see modern sets with green screens used to re-create some of the scenes.
From the wikipedia entry:
The film includes historical NASA footage as well as re-enactments and computer-generated imagery.
So as far as I can tell, no native 3D from the moon landings, just new native-3D "scene recreations" and perhaps post-converted 3D for the true lunar shots.