Just to add to my point. Ponting averages (with Zimbabwe and Bangladesh removed) 53.91 compared to Chappell's average of 53.86.
Ponting's had the advantage of playing on wickets which nowadays are flatter while Chappell played on pitches that had an extra bit of spice. He also managed to average 56 against the West Indies which at the time was a stunning achievement.
So for me Chappell.
You can probably remove West Indies post-200 as well because they've been poor, and New Zealand are arguable. Wish I had time to split his figures against West Indies and recalculate, but a lot of people do rave about current players when they play Bangladesh, West Indies and New Zealand a lot and none of those are terribly strong sides.
Pakistan are up and down so hard to justify excluding them, but then Australia hardly play them :sarcasm Ponting averaged 24.50 against them in the recent series, 63.00 down under against them in 09/10 - he's only once played them in Pakistan I believe, although he did score 119 runs for once out in that one Test.
I think any call on who is the best, second best etc is always going to be subjective. I doubt anyone has watched every batsman of all time enough let alone equally enough to judge based on watching them, and statistics across time are difficult to compare. As I've alluded to above, some players have crossed eras and runs against a pre-2000 West Indies side are worth lots more than post-2000. In fact there are three distinct eras because if you go back to pre-1991 and post-1991 runs against West Indies were worth their weight in gold with bowlers like Ambrose and Walsh second fiddle to bowlers like Marshall.