You can't really compare the Joker from Burton's film and the Joker from Nolan's. Apart from the name, they're written as almost completely different characters and are played as such. I don't think it's a case of either actor being "better" than the other.
I thought Ledger's performence was brilliant, but still just a touch overrated. My favourite performences in the Bat-franchises come from Aaron Eckhart, Gary Oldman, and Michelle Pfeiffer.