Ledger as Joker is absolutely one of the best screen villains of all time. His scenes were less about creating a psychological profile like Lecter, so I am not sure comparing them so literally is apt. But what Ledger did do is personify a very specific and modern, post-9/11 image of chaos that disturbs Americans. He reveled in it in a way that struck a nerve, and is one of the key reasons that movie is still considered by most (though not all) the best comic book movie of all time. He won a posthumous Oscar for it for crying out loud (the last time that happened was for another legendary performance, Peter Finch in Network). The life and nastiness that Ledger imbued into the Nolan version of the Joker is unforgettable. And Nolan used him well. If you want to compare him in terms of narrative function to other screen villains, he is more like the shark in Jaws. A force of nature that just rolls onto the screen and destroys the lives of everything he touches before vanishing again.
As for the Nicholson Joker, you are right his Joker is not in the same ballpark as his very best films, including Chinatown, The Shining, A Few Good Men, and One Flew Over the Cuckoo's Nest. But his Joker performance is remembered just as fondly in any retrospective as those, and more than other less iconic hits he did, like The Witches of Eastwick or Reds.
Still, my point stands. Even if it being a big blockbuster is a reason it is a highlight of his career, Iron Man and Captain America 2 were also big blockbusters. Stane and Pierce will still not be some of the roles people reminisce about when talking about them.