I think Lara played just 3 test matches against Wasim and Waqar in 97. When Pakistan toured WI in 2000, Lara was on a personal break from cricket, in 2002 when WI played Pakistan in Sharjah, and in 2003, Wasim and Waqar retired. Wasim in 99 was way past his prime, and was having a torrid time as a captain, as a bowler. Whereas Wasim in 97, although not as fast, was having a fantastic time as a captain and a bowler.
Point is, 3 test matches is just not enough to judge players of this calibre, not Lara, not Ponting. The thing going in Lara's favour is his peak coincided with the peaks of other fast bowling greats like Donald, McGrath, Pollock etc and spinners like Warne and Murali.
Ponting's peak from 2003 had no Wasim-Waqar, Ambrose-Walsh, Donald, and he wasnt as good against Murali as Lara was, I dont think anyone can dispute that. The best fast bowlers during Ponting's peak were Shoaib Akhtar, Steve Harmisson, Dale Steyn, Chaminda Vaas.
Now if Ponting was at his peak in the 1990s, how would he have fared against the bowlers mentioned above? Honestly we dont know. But based on the evidence available and the quality of the fast bowlers both Ponting and Lara peaked against, it is not fair to conclude that Ponting was a better player of fast bowling than Lara.
Maybe the 400 he got was abuse of power, maybe he did that because the series was already lost, we dont know. But thats just one example. His performances against a pretty strong South African side at home in 2003 was phenomena to say the least, he did not manage to win a test match, but the few that were draws were not abuse of power, but his batting that enabled WI to draw those matches.