I'd say Great Bay Temple.
Now, Stone Tower Temple is a very close second. It has exceptionally diverse puzzles, and the concept of flipping the temple upside down is just astounding. But something about that temple gives me a small headache, and I'm not sure what it is exactly. Maybe it's that the music can get a bit repetitive after a while, or the fact that you'll have to go all the way to the front of the temple, flip it, and go back several times throughout if you're looking to collect all the fairies, which can get rather monotonous after a while. Also the boss sucks (but it is pretty fun to kill from the ground using arrows).
However, I have no problems with Great Bay Temple. It has nice puzzles, doesn't get too tedious with the main dungeon gimmick (you really only have to switch the water current once. Only once.), and is aesthetically pleasing. Its machine-like, industrial-sounding music and its colorful lights constrasting with the dim lighting is such a step above the two previous dungeons, Woodfall and Snowhead, which were both visually and audibly dull. Yeah, the boss here also sucks, and unlike Stone Tower Temple's boss, it has no real redeeming factors, however silly they may be.
But yeah, Great Bay Temple is, in my opinion, the best dungeon in Majora's Mask.