If i target and and hit a ship that has GONK equipped, Can I use the shield token removal mechanic from the plasma torpedo to take a shield token off the Gonk card?

Thanks,

-Ben

No.

The effect of Plasma Torpedoes is quite specific: you remove a shield token from the defender. The defender is a particular ship, identified by the attacker at the start of its activation in the Combat phase.

So the shield token has to be removed from a ship, not from an upgrade card aboard that ship.