Depends entirely on how tanky your opponent is, meaning are you going to be able to use thunderbolt 4+ times or thunder 2+ times etc.
Thunderbolt kills less tanky stuff faster but thunder is better for longer battles.
Thunderbolt is superior in my opinion because you can use it more often and kill Gyarados faster. Also is great on defense.
Just comes down to play style really though, do you want to kill Gyarados faster? Thunderbolt. Do you want to kill a tanky Vaporeon faster? Thunder.