Chappell I think.
One thing I've always wondered about both Chappell and Waugh is whether one should "do a Richard" and cut their worst parts out of their career, because they're so starkly contrasted. In Waugh's case, until he broke through as a batsman with a totally new style in '89, he was pretty poor test batsman. Picked at a very young age with his bowling playing a part, though. As was mentioned earlier, he averaged 56 over his whole career from '92 on, and that's including his gradual age-related decline from the end of the 90s. Even from '89 on his record is much better than for his whole career.
But if one does that, you have to do the same for a lot of batsmen I guess. Ponting is undoubtedly a great batsman, but he looks a lot better if you take out all his tests from before '99, and even better if you take them out before '02. However, if he'd been picked fresh in either of those years I doubt his success would have been the same, since the learning curve he went through before that probably helped turn him into the batsman he became. You could argue the same thing about Waugh, in which case removing his early years might boost him more than is warranted. Maybe if he'd been first picked in '89 he wouldn't have realised he needed to cut some shots out of his game and gone on averaging in the 30s or 40s for a long time after.
Chappell also has that one horror streak where he was struggling mentally and had the underarm incident, the '81 Ashes where he elected not to tour and the home summer in 81/82 where he could hardly get off the mark. Certainly hurts his overall record.
Anyway, Chappell wins for me, hard to split Waugh and Border but I'd probably go for Waugh marginally just because I loved watching him bat so much, and his performance in the West Indies in 1995 is one of my favourite batting performances in a series. As far as Ponting goes, better to judge him when his career is over, but I think there'll be a case to rate him on par with Chappell, or the best of the four.