I can't think of anyone who can really beat Thrawn. Someone out there could give him a challenge, but he could outwit anyone. He can make something out of nothing. You would have to pit him against a Galactic Government in order to have a good match-up, and we saw what happened when he went up against the New Republic. If it weren't for the Noghri, Thrawn would have swept the New Republic aside.
If only we knew more about the Rakata. I think they'd be an interesting match for Thrawn. But, as Beni pointed out, we just don't know a ton about them.