LoY would technically (arguably?) be the
Captain Krasnok in Hate's Fury, the Scorned Maiden as HF was the "top zone" in that expac. Where it gets debatable is the spawned
Inny in Crypt of Nadox is actually a higher level mob.
Luclin is Aten Ha Ra (absolutely) but even less got to that (Vex Thal), for many it would be Seru for that xpac?
Velious is interesting... The Sleeper certainly wasn't originally implemented (though arguably intended) as the end-game encounter since it was killed "before ready" hence all the drama if you do some old post digging. Dragon Necropolis or the triad of Kael/Skyshine/Thurgadin were all upper game... but wouldn't
Tunare in Plane of Growth be the "hard encounter" most never did? Not that she was the hardest thing herself, but the whole zone aggroing with her and the faction issues...
LDoN the top raids were a series of mobs and not much was done with the content. I've seen it posted that many of the LdoN raid drops have never really even been seen. No real boss is probably the best descriptor there.