Now let me get this out of the way first off. Ash-Greninja is out due to the fact that Battle Bond requires a partner for Greninja to mentally synchronize with, and in this scenario, Greninja is not described as having a partner. (Technically, this would apply to Lucario as well, since Mega Stones typically need a Key Stone to activate it, but whatever.)
Now, that aside, there are many reasons why I think Lucario would likely win, most notably his type advantage over Greninja. Greninja is a Water/Dark type Pokémon, and Lucario has access to many fighting type moves to help him, such as Force Palm, Vacuum Wave, Close Combat, and of course, Aura Sphere. Not to mention his ExtremeSpeed, which is notably faster than even other priority moves in the Pokémon universe, and the fact that if Greninja uses something like Night Slash, it will boost his attack thanks to Justified, which can be boosted even more with Swords Dance and Power-Up Punch, and Lucario outclasses Greninja in too many ways for Greninja to counter, even if he did have access to Ash-Greninja.
Winner: Lucario