You do not want a special gyarados. Gyarados with a beneficial nature in Special Attack only reaches 240 max at level 100. If you have a Gyarados with a hindering attack nature, you can get it to have up to 314 attack.
If for some reason it does end up having higher Special Attack, if training a new one because a Special Gyarados is pretty much useless compared to other Pokemon is not an option, I guess you'd best use this:
Hydro Pump: Power is kind of neccessary here.
Fire Blast: Power.
Ice Beam: Get a x4 weakness.
Thunderbolt: Hopefully you end up facing a Pelliper.
Or you can get Dragon Dance and have a really weak physical Gyarados with normal moves that still works better than the special Gyarados.