The community generally considers the "best" way to play to be through a PC emulator with specific mods that restore original N64 mechanics lost in the 3D remake.
If you have a physical 3DS or a digital copy, the setup is more straightforward. The Legend of Zelda: Majora’s Mask 3D ROM & 3DS...
To play , you can choose between original hardware or an enhanced experience via PC emulation. Emulation & ROM Setup (PC) The community generally considers the "best" way to