Honestly, Sableye and Klefki are overall better prankster support, but of the two Thundurus, with it's superior defensive typing, access to thunder wave and nasty plot and more reliable STAB is superior.
Thundurus @ Life Orb/Leftovers
EVs: 4 hp 252 sp atk 252 spd
- Thunder Wave
- Thunderbolt/Volt Switch
- HP Ice / Focus Blast / Grass Knot
Being outclassed as a defensive prankster abuser, thundurus is best as an offensive one, especially with that base 125 Sp Atk and high speed tier. Thunder Wave is far better at managing speed than Tornadus's unreliabble Tailwind in singles, and Thunderbolt is a far more reliable STAB than Hurricane. Volt Switch is also useful, granting Thundurus free switches. Taunt and Substitute are also both fine Prankster options, taunt ruining walls and set up sweepers and substitute allowing for scouting and offensive presence. The choice of coverage is the hardest. Although it is weak HP Ice is great for Landorus, Gliscor and Garchomp, all three of which are extremely common. Focus Blast nails Tyranitar, Ferrothorn and Heatran nicely. Grass Knot may be used as a more reliable Tyranitar check, and can hit Gastrodon and other water/grounds nicely as well. It should be noted that it is ineffective against Rotom-W