That's a bit of a tricky question.
In terms of the "new" series, it's definitely Davros as the master was a bit ... underused.
In the classic series,
Davros had a couple of good stories Genesis, Resurrection, Revelations and all the rest weren't great appearances.
The master had some good ones; Daemons, Terror of the Autons, Colony and Frontier in Space, Sea Devils, Deadly Assassin, Keeper, Logopolis and a lot of other reasonable ones. There weren't too many truly dreadful "master stories".
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In terms of the best villain ever... I don't think it's either... IMHO, I'd be more likely to choose someone like Sutekh.