I think, at each's best, it's basically a tie. Malkin's 2008-09 season, RS + playoffs, is probably as good or better than any stern-to-stern season Ovechkin has had, and Malkin's 2010-11 is up there, too. On the other hand, Ovechkin's 2007-08 is likely as good or better than any Malkin regular season.
Looking at extended primes, statistically...
Malkin 2007-08 to 2019-20 (RS only):
1.20 PPG
Ovechkin 2005-06 to 2018-19 (RS only):
1.12 PPG
Ovechkin comes out a bit better in plus/minus; Malkin comes out a bit better in playoffs, partly due to four Cup runs.
Overall, about even. I mean, I guess if push comes to show Ovi gets the higher ranking because of better longevity (and durability). But at each's best, I call it even.