Molten Core: Ragnaros
Blackwing Lair: Nefarian
AQ20: Ossirian
AQ40: C'thuun
Naxx: Kel'thuzad
Karazhan: Nightbane
SSC: Vashj
Tempest Keep: Kael'thas
Mount Hyjal: Archimonde
Black Temple: Illidan
Sunwell Plateau: M'uru
Naxxramas: Kel'thuzad
VoA: Lightning
Ulduar: Yogg-Saron
TotC: Anub'arak
Icecrown Citadel: Lich King
Blackwing Descent: Nefarian
Throne of the Four Winds: Al'Akir
Bastion of Twilight: Sinestra
Firelands: Ragnaros
Dragon Soul: Spine
Mogu'Shan Vaults: Will
Heart of Fear: Amber-Shaper
Terrace of Endless Spring: Sha
Throne of Thunder: Lei Shen
Siege of Orgrimmar: Klaxxi
Highmaul: Imperator (mechanically harder, Butcher was the overall hardest boss to down though)
Blackrock Foundry: Blackhand
Hellfire Citadel: Archimonde
Emerald Nightmare: Cenarius
Trial of Valor: Helya
Nighthold: Gul'dan
Tomb of Sargeras: Kil'jaeden
Antorus: Argus
Uldir: G'huun
I think the question is fundamentally flawed. There are almost no raid instances in the games history where the final boss was not the most difficult one. You can get into the argument of what constitutes difficulty, but sheer mechanical complexity is what constitutes difficulty imo. I don't think there is much room for changing much from the list I have made, if you look at objective difficulty.