2 mods are required in order to play as a pony in Fallout 4.
Crimes Against Nature (CaN): http://www.nexusmods.com/fallout4/mods/19040/?
RaceCustomizer: http://www.nexusmods.com/fallout4/mods/15212/?
Be sure to heed the warning message that appears after your game loads too because you receive a holotape that helps with modifying your character.