Ninjask: if you teach it protect its speed boost ability will kick in and should outspeed deoxys. (Have max speed and attack evs).After that hit it with a x-scisor or set up a swords dance if it's a defense form.
Prankster thunderous: start off with a T wave then attack. Even if thunderous goes down, you have crippled deoxys.
There more options ,but it's more likely that deoxys will be switched out before facing a threat. Entry hazards may be a good idea. Also it's important is that you keep in mind all of your friends party Pokemon.
Also I would have said in the question if it use special attack or attack.