I'm going to put my vote on Swain. With his sudden coup of Noxian leadership I think there is going to be a dreadful turn of events during his rule, maybe even start another war between Demacia and Noxus.
Malzahar could be second place, with all the void mumbo jumbo he's spreading about.
I don't know enough about Mordekaiser to really rate him as a villain. He doesn't seem to be a major threat.
Malzahar and the void are unknown quantities...
Mordekaiser is meh now that his lore doesn't specifically have him originating in the Shadow Isles.