The Doc is correct! The specific answer is the non-possessed Pirate Commando due to the perspective used in the riddle.
The strongest and fastest of my kind, - Only the best Space Pirates can become Commandos.
Wielding the greatest technology offered, - Up until Prime 3, Commandos used the best weapon technology the Space Pirates had up to that point.
I am contested over by the strongest of monsters. - This is the key to the riddle: the Dark Pirate Commando entry states that only Hunter Ing are allowed to possess Pirate Commandos, and that the competition to possess one was fierce among them.
Whether by my own hand or that of others, I hunt the greatest among enemies. - Pirate Commandos have pledged to hunt down and kill Samus, their greatest enemy, and they do this regardless of whether or not they have been possessed by the Ing.
Take it away, Doc.