Well it all depends on what your specialization within the broad field of International Relations that you wish to study. www.aspia.org should list the best IR member schools, but you should still check the affiliate members. Hope the link helps.
Top PhD Programs in International Relations (Foreign Affairs Reputation and Ranking Study)
1) Harvard University (Cambridge, MA) [Kennedy]
2) Princeton University (Princeton, NJ) [Woodrow Wilson]
3) Columbia University (NYC) [Columbia School of International & Public Affairs]
4) Stanford University (Palo Alto, CA) [Freeman Spogli Institute @ Stanford]
5) University of Chicago (Chicago, IL) [note: link is to their masters program: Committee on International Relations & the U of C]
6) Yale University (New Haven, CN) [Jackson Institute of Global Affairs]
7) University of California, Berkeley [International and Area Studies]
8] University of Michigan (Ann Arbor, MI) [see also: international policy center at michigan]
9) University of California, San Diego [School of International Relations and Pacific Studies] (course of study in IR)
10) Cornell University (Ithaca, NY) [see also: Mario Einaudi Center for International Studies]
11) Massachusetts Institute of Technology (MIT) [Center for International Studies]
12) John Hopkins University (SAIS/ Washington DC) [School of Advanced International Studies]
13) Georgetown University (Washington DC)
14) Duke University (Durham, NC) [Duke Grad. Political Science]
15) Ohio State University (Columbus, OH)
16) New York University (New York, NY)
17) University of Minnesota (Minneapolis, MN)
18] University of California, Los Angeles [Burkle Center for International Relations]
19) Tufts University (Medford, MA) [Fletcher School of International Affairs]
20) University of Rochester (Rochester, NY)
Top 20 Masters Programs in International Relations (Foreign Affairs Ranking and Reputation Study)
1) Georgetown University (Washington DC)
2) John Hopkins University (Washington DC)
3) Harvard University (Cambridge, MA)
4) Tufts University (Medford, MA)
5) Columbia University (New York, NY)
6) Princeton University (Princeton, NJ)
7) George Washington University (Washington DC)
8] American University (Washington DC)
9) University of Denver (Denver, CO)
10) Syracuse University (Syracuse, NY)
11) University of California, San Diego
12) University of Chicago (Chicago, IL)
12) Yale University (New Haven, CN)
14) Stanford University (Palo Alto, CA)
15) University of Pittsburg (Pittsburg, PA)
16) University of California, Berkeley
16) University of Maryland (DC/MD ?)
18] Massachusetts Institute of Technology (MIT)
18] Monterey Institute of International Studies
20) University of Southern California (Los Angeles, CA)
Source:Wordpress.com/2010/11/26/top-phd-programs-in-international-relations/">http://compassioninpolitics.Wordpress.com/2010/11/26/top-phd-programs-in-international-relations/
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