For Ocarina of Time, Water Temple wasn't really hard. People are just impatient and complain just because it gets a little annoying changing the water level. Then people complain about missing the keys. That's why you have the
MAP and
COMPASS. There were a couple tricky parts, but nowhere near hard.
As for the hardest in OoT, I don't know. They were all sort of easy. I guess I have to say Ganon's Castle and Tower. It's not hard, but it's not as easy as the other ones.
However, I actually found MM dungeons fairly challenging. When it comes to puzzles and secrets, I had to think harder and more outside-of-the-box in that game's dungeons than I ever had to in most of Ocarina of Time. It even got to the point that I would call the last two dungeons (3 and 4)
hard because of that. I even remember a part where I had to LET a Dexihand pick me up and
THROW me up to a ledge that you have to get up to.
I had more and more trouble as I went through each new dungeons, so the fourth and last dungeon, the
Stone Tower Temple, was my hardest dungeon out of Oot and MM.