There's a huge thread on this topic including the new Foreign Policy Magazine rankings.
Ranking International Relation Programs
Some observations made:
1) JHU's Paul Nitze School of Advanced International Studies (SAIS), arguably the top IR Master's program, is at a separate campus from JHU Baltimore. It was a school established separately to train foreign service officers and then in the late 50s or early 60s tried to affiliate itself with its namesake's alma mater, Harvard. But Harvard refused and SAIS became JHU's tremendous gain. JHU's undergrad is probably not listed for this reason. And the following....
2) Most undergrad IR programs exist at PhD type academic powerhouses according to this ranking within Poli Sci departments. Therefore, good Poli Sci undergrad programs tend to = good ranking.
3) Likewise for PhDs, broadly speaking the best ACADEMIC IR programs largely overlap with the best Poli Sci PhD programs.
4) The Master's programs are more practically and policy oriented. Therefore, places like Berkeley, which don't even have a Master's program in IR are ranked, for instance, at the bottom of the top 20 in this category simply because a few of the respondents didn't even realize it doesn't have such a program and ranked it anyway.
5) I believe personally that such reputational confusion marked Georgetown's ranking at number 1 for a Master's. Admittedly my experience is out of date (by about 10 years) and I'll admit my potential bias, but it was my strong impression when I was in DC going to SAIS that Georgetown, while widely acknowledged to be tops as an undergrad institution, was not considered at the top for an IR Master's. On the other hand, its undergrad I think is ranked too low on the undergrad ranking. For a school which mixes policy and theory and which has a top-rate undergrad student body in IR (the BSFS program admits separately as I understand it), Georgetown should be at the top of this list, in my opinion.
6) These programs should have been separated, in my opinion, into THEORETICAL/ACADEMIC vs. POLICY/PRACTICAL. Then you'd see programs like Fletcher and SAIS appear differently, particularly at the PhD level. Yes, as strange as it sounds, there are people who get PhD's with no intention of going into academe.