IR undergraduate rankings for Brazil are quite debatable, and USP leads the last one. In General USP and Rio Unis have the best brand value overseas. Nonetheless, Federal Universities are well-regarded. You should get a letter of recommendation from Paulo Visentini, he was Rio Branco Chair at Oxford recently. Reis da Silva has taught at SOAS and did his PhD at Leiden which is well-ranked.
Just a quick question, since application season is now underway. My grades were meh in my three undergraduate years. Then I improved and my Master's dissertation was summa cum laude (overall degree: magna cum laude). Is a sharp improvement over time good, irrelevant, or bad (admissions committees look for anything to eliminate you, I guess)?
Well, just look at the affiliations of those who publish in the Hague Journal of Diplomacy. But you don't need an advisor that's a specialist, by the end of the PhD you'll know more than him anyways.