Congratulations, you have a wonderful choice ahead of you.
My own opinion is that, if your ultimate ambition is to get a job in a political science department, Harvard would be the better choice. Not only will you receive a Harvard theory education (which is great even if you don't end up working with Mansfield, as someone mentioned above), you'll also be able to make use of all the other resources in the department when completing your degree requirements (like the minor). If you're at Harvard you'll have access to IR/comparative/american/methods scholars of the very highest caliber. This should ensure that you'll get a top notch all-round training in political science, which is essential for landing a good job in a politics department.* Don't underestimate how important this is! When you finally get to the job market you'll need to be able to convince hiring committees that you can talk knowledgeably to non-theory political scientists about things like quantitative analysis, formal modelling, game theory etc., since these methods have such a grip on the discipline of political science as a whole (if you're interviewing at a small school, your hiring committee may itself contain one or more non-theorists!). A poster above made some cryptic comments about polisci departments hiring from philosophy departments or from the UK. I don't think this is widely the case at all. Perhaps Ammar could say more about what he means, and provide some examples.
The Committee on Social Thought is indeed (in)famous, and I'm sure it's a fabulous program for the right sort of candidate, or if you are undecided about what sort of department you want to teach in. But it is very unusual, it's notoriously lengthy and difficult to complete, and I can't think of many (if any) well known political theorists that have come from there recently.
Best of luck.
* PS I'm not saying you couldn't get a rigorous political science training at Chicago. Obviously, their own political science department is as good as (and for some particular subjects, better than) Harvard's. I just don't know how much access you'll have to it as a CST student. Perhaps you could email some current students at Chicago to find out?