I think for a Ph.D. program, it's hard to state the rank. A Ph.D. program in a specific specialization is said to be excellent (or good) if the research area is diverse, the faculty in that particular program has been publishing in top-tier academic journals related to the field (in the I.S. field, these journals would be, for example, MIS Quarterly, ISR, Communications of the ACM, Decision Sciences.), and (not necessary) there are some big names (faculty) in the field of your interest. The ability to produce research published at a top-tier academic journal shows a faculty's significant contribution in that particular field, although there are some "politics" that allow someone to publish in top-tier academic journals (usually faculty at top schools produce research at top-tier academic journals. I know an I.S. faculty at MIT who is a frequent "author" of MIS Quarterly. Her publications are always listed as reference by other I.S. researchers. But this is not an absolute phenomenon.).
For example, as you said, UConn has a better rank in I.S. than Rochester has. These two universities are a top-tier and a tier-2 universities. On the other hand, this is based on USNews.com, Georgia State University ranks a lot higher in I.S. program than the other two, while its Robinson College of Business is not even listed as a top business school (and GSU overall is even listed as a tier-4 university). This is because at GSU, there are several big names in the I.S. faculty (I can mention you some, but I don't think it's appropriate to mention their names here) who have a great contribution in the field of I.S.
I suggest that if you want to choose, you will have to choose based on the faculty's research interests that match with yours the most (and also the scholarship
) It is safe to choose a school that the faculty in the I.S. program has a diverse research area. Some of the schools that I know, whose faculty has a diverse research area, are the Univ. of Maryland - College Park and NYU (GSU does not have a research area in economics of I.S. The faculty who used to do research in that area has moved to work in Europe). In my statement of purpose, I specifically mention my research interests would be I.S. development, e-commerce, management of software engineering, and economics of I.S. and I also implicitly mention my dissertation topic (and then, based on interviews with several schools, the faculty seemed impressed, but they mentioned that it is still far, too premature to state a dissertation topic).
I mentioned earlier that I also apply to UConn, but I looked at the faculty's profiles and research interests, and none of them has research interests in software engineering/development, but they put Computer Science's Advanced Software Engineering as a research method course (which to me, is sort of odd). I didn't really look at Rochester as I don't apply there. But couple of months ago when I was choosing which schools I wanted to apply to, I visited Rochester's website to see the I.S. faculty's research interests and dissertations produced by graduated Ph.D. students, and I can conclude that their research interests are more on the organizational and behavioral tracks, or specifically, digital market and e-commerce. In my humble opinion, the research area in the I.S. program at Rochester is not diverse. I personally look for a school that has a combination of technological, organizational, and behavioral tracks. Well, the decision is up to you though, and you know my answer would be that if I were you, I would choose UConn (this is a subjective suggestion because I'm also applying there
). The I.S. research area in UConn is more diverse than that in Rochester (please look at the faculty's profiles of both schools and compare them. Try to look at their research interests and the academic journals to which they published their research). Thanks.