>>31216089Ash-Greninja was created by Game Freak.
http://www.serebiiforums.com/showthread.php?654751-Pok%E9mon-the-Series-XY-Pok%E9mon-the-Series-XY-amp-Z&p=18312722#post18312722>*Yajima wanted to make the bond between Satoshi and Gekkouga a major part of the story, but felt it would be difficult to do so if it had to remain a Gekkouga, so he went to Game Freak, and they came up with the idea of a synchro transformation. It was put in Sun/Moon afterwards, but was created during this discussion between anime staff and GF.Yajima wanted something special for Ash's Greninja, so he went to Game Freak, and they came up with the Ash-Greninja form.
Game Freak played a part in its creation. It's not a 100% anime-original thing, so yes, I'd say it's canon.