Irfan Nooruddin

I am not aware of an APSA ranking, though that's not to say it doesn't exist. At this point the US News rankings are pretty much the only widely available rankings of which I'm aware.

Yeah, no. I've served on admissions committees at Michigan, Ohio State, and now Georgetown. I can unequivocally tell everyone here that this inference lacks truthiness. As to the OP: Impossible to know, of course, but IME admissions committees weigh more recent academic performance more highly than earlier years, and a clear break is actually to your advantage because it indicates that something fundamentally changed between your AA degree and the BA completion. Either way, no point worrying about what you can't change. Best of luck.

Universities very rarely if ever hire their own PhDs; and all tenure-track searches tend to be national searches. So if your goal is to obtain an assistant professor position at one of those four universities, the advice would be to go to the best PhD program you can go to

I agree with MrsPhD's advice. Department --> Subfield --> Advisors: you get admitted to a department, and within it you choose a subfield. That dominates the first 2 years of your program. But the bulk of the time you're in graduate school is spent working with your advisor and a committee of 2-3 others. Those are the people who will have the biggest effect on your research and placement potential. Of course, there are halo / reputation effects from a highly ranked department that boost all candidates coming out of that program so in a perfect world the choice of best advisor for you and choice of department ranking are not completely at odds with each other.