There isn't really a dungeon that sticks out in this game like in most of the other installments of Zelda in terms of difficulty, at least for me. I guess Fire Sanctuary would be my choice because it's long, integrates most of the items from earlier dungeons, and has the hardest boss in the game IMO.
I'm voting for the Earth Temple because I died way too many times in that dungeon while in Hero Mode. The other Dungeon I found rather tricky was the Sanship, some of the puzzles had me confused at times.
I didn't find the Ancient Cistern hard at all. But, it is my favorite dungeon of Skyward Sword, I absolutely loved it. But the hardest was definitely the Sky Keep. It took me hours and hours to finish it. A genious huge puzzle!
I'm gonna have to say the Lanayru Mining Facility. Sure, it wasn't filled with hoards of enemies, but the puzzles required some real thought and careful footing, as well as avoiding numerous traps. The Sky Keep is a close second for me, most definitely, but I just believe the Mining Facility is the most challenging overall.
I didn't find any of them to be too difficult. The thing that got me in this game were Silent Realms. I loved them after I completed them. I hated the nerves of knowing you have to be chased in order to get some tears.
I actually found Lanayru Mining Facility to be the toughest dungeon to figure out, mainly because of all the Timeshift Stone puzzles which were only moderately used outside the dungeon. In second place is the Sky Keep, for it's room rearranging puzzles, and in third is the Sandship, again because of Timeshift Stone puzzles, although I think it was easier to figure out because it has only one Timeshift Stone, whereas the Mining Facility seemingly has one for every other room.
Skyview was incredibly hard for me. The dungeon was like no other I have ever played. I went into the depths of insanity...only to find an even worse...emaciated man awaiting me, speaking of what I assumed to be my girlfriend. He violated me as he went behind me, threatened to kill me...he even licked his lips – some confused lust for my sword I guess. That's all..
Speaking seriously, Sky Keep did me in. If I hate anything, it's shifting rooms around. I had to do that in Star Ocean 3, to have to do it in Skyward Sword made it even worse. Granted, Sky Keep was relatively small but...it was still a mind warper for the moments I was in it.