Stone Tower Temple from Majora's Mask > every dungeon in OoT. I'd say every dungeon in MM is better than every dungeon in OoT, as well.
On my recent play through, Stone Tower was significantly less impressive than I remembered. It's easily MM's best dungeon (which isn't saying much, honestly), but doesn't hold a candle to any of adult Link's dungeons in OoT.
And every dungeon better? Seriously, dude? Woodfall is in no way better than the Forest Temple, The ice dungeon (whatever it was called) had some cool puzzles but wasn't really stellar, and Great Bay Temple was far worse a water temple than the Water Temple.
Come on, son. 
I think MM has better dungeons because they fully utilize your item set. OoT has a lot of pointless items and most of the dungeons are nothing but filler. In MM, all three masks work up to make a very cohesive experience that constantly builds upon each other. Also, MM doesn't waste any time. You learn any and all pertinent information for the dungeon before even going into the dungeon. That's very helpful, because unlike OoT, which always does the Zelda thing where it has to teach you how to use the item in the middle of the dungeon, Majora's Mask says fuck that, and just ramps it up to 11 from the first dungeon.
I think it depends on what you want or what kind of Zelda dungeons you prefer. MM dungeons tend to have better sense of exploration (fairies, mask abailities), as well as replay value (fairies). OoT is pretty flawed. How many times do you use really use the Lens of Truth outside of the Shadow Temple? A flaw in OoT design. How many times do you use the iron boots in OoT outside of the water temple? Another huge flaw in OoT design. We can do this repeatedly for practically every dungeon aside from a few. Majora's Mask however? Consistent, and it incremental difficulty that continuously builds upon the previous dungeon. It is superior in every way.
The only thing I think OoT does better than MM is boss fights. Exploration, dungeons, abilities, itemization, sidequests, story, characters, writing, music, map and locales, replay value. Majora's Mask is superior in every way. My opinion.
Also, Great Bay is worse than Water Temple? Water Temple sucks. Aside from my post about the iron boots, the temple is just one giant labyrinth that isn't challenging or anything, aside from placing one treasure chest behind a single tomb/crest/whatever. What is great about the Water Temple aside from Dark Link? It's a bad dungeon.
