I think, without having watched the series and judging mainly on comments, that Flintoff's performance in India wasn't quite on the Ashes level individually. He obviously batted very well and his bowling was pretty good to, but he didn't take a huge number of wickets or make any really big scores, it was just consistent rather than brilliant. Ponting on the other hand has been carrying Australia's batting recently, and he played two tests in March, one of which was on a seamer and he made 74, and the other had a century in each innings. And obviously, he averaged 70 in ODIs as well.
I guess it depends on your criteria. I think judging the players themselves its hard to argue that Flintoff had a better month than Ponting. He did well, but Ponting was unstoppable in both forms for the whole time. Flintoff's team achieved more, certainly (though a whitewash in South Africa is nothing to sneeze at), and you could possibly argue that through his leadership he had a bigger impact on that success than Ponting did. That's a pretty subjective call, but I think I'd have to go with Ponting, as March really capped off an amazing six months for him and individually he was more successful, as well as being hugely important to his side. He also did it in both ODIs and tests, rather than just the one form.