They are both good Pokèmon, but I'd say that Ninjask is a good Baton Passer and Shedinja is an invincible wall . First up, Ninjask has almost unbeatable speed, even with a speed lowering nature. It has extremely low defencive stats, so its best to give it a a Focus Sash. Ninjask has the ability Speed Boost. Take advantage of the ability with this moveset:
Ninjask@Focus sash. Speed Boost
Protect: Painlessly activate Speed Boost.
Swords Dance: Raise your attack
Baton Pass: What do you do with all of that Attack? Baton Pass it!
X-Scissors: To do damage.
Next is Shedinja. 5/17 types hurt Shedinja. Just send Shedinja out as your last Pokemon, it may work. Here's my Shedinja moveset:
Shedinja@Focus Sash. Wonder Guard
Confuse ray: Confusion is awesome.
Toxic: Bad poison really hurts.
Will-O-Wisp: For Steel and poison types.
Dig: For Heatran and also to just be underground, waiting out the poison/burn.