According to this source, there is no source:
No discussion of Jewish attitudes toward Aristotle can be complete (not that this essay aspires to completeness in any event) without mention of the infamous, scurrilous "Rabbitstotle" legend of the great philosopher being caught devouring a live rabbit, and responding to his surprised observer that "I am (or: 'this is') not Aristotle"; but although this story is quite widespread in contemporary frum circles, I have yet to locate any source for it whatsoever, even an unreliable one, and I once (reasonably discreetly) walked out of a lecture by a very prominent speaker in frustration at his confident assertion of this libel (or one of its variants) as fact. This ridiculous anecdote has even been attributed (comment #46 to this article) to, of all people, Rambam (!)...
In a comment on that post, a reader suggests:
Perhaps the "Rabbitstotle" legend of the great philosopher being caught devouring a live rabbit,has been confused with the well documented story of Nevuchadnetzar being caught by Tzikiyahu Hamelech doing the same type of act. See: Nedarim (65a), Midrash Tanchuma (Va'eschanan, 1), Ben Sira (II).