What would be considered canon in the Pokemon franchise? Usually we would treat the manga as canon for most works, but as most people usually only have watched the animation or played the video games, would in this case the manga still be considered canon over the anime? Or would it be the videogame and manga based on it?
Canon usually refers to the original work rather than the most popular one. As such, I would imagine that the original Japanese manga is canon.

The other mediums can be canon as well; the anime for example is a very important part of the franchise. Stil, the manga would probably still take precedence.

Canon is a very broad term that can be as strict or lenient as the user who uses it, so it's hard to answer this question definitively.