Well I am a victim of TopThundy myself and I was also wondering what could stop this annoying duo. I am almost sure that this lead can wall TopThundy. Anyway here it is:
Rotom @ Choice Scarf
EVs: 4 HP / 252 SpAtk / 252 Spd
- Volt Switch
- Shadow Ball
- Hidden Power [ICE]
Well Trick will force Hitmontop into using Fake Out until it's switches out whiles it will lose it's gem meaning that it wouldn't hit that hard with Close Combat. Volt Switch is to switch out to a safer option should it be needed. Hidden Power ICE is to deal some damage against Thunderus. Shadow Ball is a more powerful STAB that will deal some damage against common doubles Pokemon such as Jellicent, Dusknoir, Cresselia etc..
Amoonguss @ Black Sludge/ EDIT: Mental Herb
Trait: Effect Spore
EVs: 252 HP / 88 Def / 52 SpAtk / 116 SpD
- Sludge Bomb
- Rage Power
Well I was thinking of Effect Spore over Regenarator just to cripple a lot of physical sweepers into sleep as there is a vast 30% chance of any Pokemon hitting Amoonguss to fall into a deep sleep. However I am aware that Regenarator is often prefered over Effect Spore. Spore is just incase Hitmontop doesn't fall asleep whiles using Fake Out. Sludge Bomb is a nice STAB move should Amoonguss get taunted by Thunderus (notified by X-Charizard). Rage Power is to help Rotom avoid any dangerous, threatening move. Protect is just to avoid the any moves that Amoonguss doesn't appreciate.
I think this could actually work out but I am not 100% sure though