I think Thanos topped Joker in Endgame. It pushed him over the edge for me.I still have Joker (Dark Knight) as the GOAT comic book villain, but Thanos is probably #2.
As far as him being topped? Maybe Doom if they actually do him right.
Joker is entertaining chaos. Thanos got a whole movie devoted to developing him Infinity War and then a half a movie to solidify him. He's just a more rounded character than Joker was.