I think the debate of Water Temple vs Great Bay Temple can go on forever, hehe.
I stand by my opinion in thinking the Great Bay Temple was harder, and it was also longer. Think of it this way, after beating both temples several times, playing through them again and getting everything in the Temples, it would take a longer time to beat the Great Bay Temple.
In Ocarina of Time there are a few skulltulas, one mini-boss, and then the dungeon boss. While in Majora's Mask, there are the 15 stray fairies, two mini-boss battles, and then the dungeon boss.
Heck, once you master the Water Temple, you'll be spending more time putting your iron boots on and changing the water level than actually playing, hehe. At least in Majora's Mask, didn't have to change the water direction much.
All in all, these were two my least favorite temples in both Zelda titles. Not so much because they were hard, I just never was too found of 3d water dungeons in the first place. But still, I think Great Bay Temple was the hardest of all the N64 Zelda dungeons.