On the whole, the dungeons in Majora's Mask were more difficult. The enemies seemed easier, because most of them were recycled from Ocarina of Time or incredibly simple to defeat with the various transformations, and the bosses were much easier, but the dungeons, specifically the puzzles and Stray Fairies, were harder.

Lots of people see Ocarina of Time as harder, but that's because they confuse length with difficulty, and because Majora's Mask is a lot easier for veteran Ocarina players.