If you're going to want to Sweep the opponent, I'm already assuming that you're going to use an attack form deoxys, being that it has the HIGHEST attack stats in all of pokemon. It also has the 3rd highest speed apart from deoxys speed form and Ninjask.
-Awesome Attack stats
-Can Learn Many Powerful Moves
(Bolt/Beam Combo as well as Superpower, Psycho Boost, etc)
-He really can't take a hit (In attack form)
Overview: If you're choosing deoxys, you have to hit hard and fast. Watch out for scarfed pokemon and priority moves, because deoxys won't get a second chance.
Definitely one of the most formidable special attackers in all of pokemon. though it's special attack and speed doesn't out-do deoxys, at least he can take a hit. Mewtwo is more more traditional in his stats than deoxys as an uber, so he is given a little bit of defense.
-Awesome Special attack
-Very good speed
-Can be made specially defensive (W/calm mind, amnesia)
-Also has access to powerful moves
(Bolt/Beam combo, Psystrike Aura Sphere etc.)
-Doesn't hit as hard as deoxys (nothing does)
Overview: Mewtwo can withstand powerful moves better than deoxys, and even though nothing has the attack power that deoxys does, mewtwo's sp. attack is still good enough to sweep.
Conclusion: Though either pokemon would suffice as a "Sweeper," Mewtwo would probably last longer in the battle.