Majora's Mask. Period.
OoT was undoubtedly great. But my god, Majora's Mask had an atmosphere that cannot be combated. The music and environments were overall much better than OoT, imo.
There's also the matter of the plot. I absolutely loved all of the plotlines in MM to bits. All of those silly little sidequests had stories behind them that gave meaning to it all, and it was refreshing to see a non-ganon based main plot. The whole three-day system was brilliant in my opinion, added urgency and a mysterious quality, seeing as everything you do was reversed when you went back in time. And for some reason, I found that MM was able to play on emotions far better than OoT. Just the little things too, not the big things. Like finding the swordsman in the training school during the final hours before the moon crash, that felt genuine. A feeling I hardly ever felt in OoT.
I still love OoT, but MM truly has my heart.