The implication is that it was Mad-Eye Moody who lost a buttock, yes, but nowhere in the series does it explicitly state this as fact.
The other candidate for losing a buttock would have been Fred Weasley:
‘You die,’ said Ron simply. ‘Fred and George tried to get me to make [an Unbreakable Vow] when I was about five. I nearly did, too, I was holding hands with Fred and everything when Dad found us. He went mental,’ said Ron, with a reminiscent gleam in his eyes. ‘Only time I’ve ever seen Dad as angry as Mum. Fred reckons his left buttock has never been the same since.’
Half-Blood Prince - page 305 - Bloomsbury - chapter 16, A Very Frosty Christmas
However, this language implies that Fred retained his buttock, even if it didn't remain in its original condition.
I still err on the side of Moody being the one to have completely lost a buttock. Moody is undoubtedly a better wizard than Tonks is a witch, who is in turn a better witch than Fred Weasley is a wizard, purely through experience's sake at the very least. So if a better wizard than Tonks has lost a buttock, my money's on Moody's bum being the one to have taken the hit.