I had thought these were the same, but my dictionary says as follows; in most cases, あいまい is used in the context that the subject is intentionally makes things ambiguous. So the word can be replaced with equivocal. On the other hand, あやふや implies the subject is unsure what’s what, and seems to be unreliable. By the way, here is another similar word, うやむや. The word emphasizes stronger equivocality than of あいまい.