OK, here's my take. I Went to MAPSS (I was in your same position deciding between UChicago, New School and Berkeley for MA). I really loved it. It really did help me towards being prepared for a Phd degre and I got 3 letters of recommendation from UChicago faculty. Now, when I applied to Phd programs I didn't do too terribly well, but I think that has to do with the current economic context as well. I know some people who, after doing MAPSS, have gained entrance to places like Berkeley, Columbia, Harvard, Yale and to the University of Chicago itself.
My thought is that it is an extremely good program, but a lot of it is going to be based on how well you choose your courses (because you can basically take whatever you want), how well you do at them and how good of a relationship you build with your professors. Unlike some of the people who have commented about MAPSS here, I never had a problem choosing an advisor, nor did I ever feel that I was shunned away for being a MAPSS student (and not, say, a Phd), but then I developed a good relationship with every single professor that I worked with and participated in class. In other words, you will probably get a lot out of this program, but you have to work your part as well.