i put him on a set, 99.

AA, KK and QQ are obviously very unlikely... maybe he has JJ and this is probably the only likely holding you beat?

Other than that you beat a bluff if he thinks you have AK/AQ unimproved but this is quite unlikely due to your check-raise (not a common way to play ak/aq unimproved)

You made a simular post a few days back (maybe you hade overpair instead of 2pair), where you called at the flop and the villan did have the set (3's i think?) I think this is a situation where you can sniff the set and make a disciplined fold.

Another consideration is you both have fairly deep stacks and if you dont fold your stack will deffinatly be allin on this hand.