Note: Keep in mind that the anime has no set attack values, some moves like quick attack and arial ace can deal way much more damage and could OHK even tho they're relatively weak moves in the game. Heck sometimes moves can be combined in the anime to deal a crap ton of damage to pokemon... not to mention that there's no accuracy stat in the show as well XD
If this is just a head to head fight against Greninja and Charizard without Ash's support (So no Ash-Greninja). Charizard might win...
Charizard has proven to take a ton of punishment, it's insane how tanky it is, even taking water attacks head on. Not to mention how hard Charizard actually hits. It can easily OHK weakened tanks with Seismic toss (Which also has a flaming variant that does a lot more damage). Now Greninja is a strong Pokemon on its own, not to mention it probably has the highest will power among Ash's pokemon... but without Ash's support, it can't match Charizards training and Experience. Not to mention greninja is a complete glass canon...
If Greninja has Ash's support (and has access to Ash-Greninja) hands down, Even if Charizard has the support of an Ash of his own, I believe Greninja wins this fight hands down. Ash-Greninja can consistently overwhelm other mega forms(Which are just as strong as legionaries) with its blistering speed. It's hard to hit him because of his speed, but he's also a master of Shadow Clones (Double team... man English localized names are so boring at times) Not to mention all the perks the bond phenomenon gives greninja, he has practically no blind spot (As he sees what Ash sees), Greninja could also tap into Ash's combat experience as the two of them are practically one being during the phenomenon. And it has that Giant water shuriken as a finisher (I WISH USUM HAS THAT AS A Z-MOVE!!!)... It'll easily overpower charizard with his Ash-Greninja form in my opinion.
Now if Charizard could mega evolve tho... now that would be an interesting battle XD