Geez, I go away for a few months and look what I miss.
Ray Harryhausen has said that the shots that you are referring to have the real Empire State building in them. Like Ted, I have never seen that angle of the building in another photo or film. The city scape is a painting,  so the building could, and most likely is one. I am sure however that the building is not a miniature.
There is no doubt that Kong is optically added to that shot, the planes are most likely as well. Since Kong is printed onto the shot, there is no need for the Kong to be the same size model going up and then down. I too find it hard to believe that the could have had the camera going fast enough to capture that slow motion of the little wooden jointed Kong falling, and have it come out like that in the film. Also the little Kong would have probably bounced all the way to New Jersey after hitting the first ledge.
Kong on the way up looks like no other animation in the film, no character, no life, in fact it looks like no stop motion or go motion that I have ever seen.  If it was animated, then I would think that it was cartoon animation. His legs also appear to be much longer than the Kong models. The movement is very smooth, which does not mean that it is live, but with all of the other factors combined, to me it  looks like a guy in a suit. Also, having said all that, it is likely that the suit that went up the building went down it as well, as that looks a little funky as well. 
Great topic by the way.
I am going to side with Don and Ted on this one.

Tim