We're talking about a Pokemon that couldn't even defeat Mega Charizard. How is that thing stronger than Charizard or Sceptile, both of whom defeated Legendaries? Try again.
Are you seriously suggesting that a wild untrained Articuno is stronger than a Mega Charizard X who defeated 10 Mega Evolved Pokemon in a row, including one Mega Houndoom belonging to the Kalos E4 member Malva? Alain's Mega Charizard is easily beyond E4 level and there is no way in heck a Frontier Brain level Articuno holds even a candle to it. While defeating a Legendary Bird is still impressive from Ash's Charizard, the Legendary Birds are easily among the weakest tier of Legendaries and no way they would hold even a candle to E4/Champion level Pokemon like Malva's Mega Houndoom, Alain's Mega Charizard X or...say Kalos Champion Diantha's Mega Gardevoir. I mean that shouldn't even be an argument, a certain Zapdos was feeling significant pain from a Boomburst from Ash's freaking Noivern. I'd rather say that let alone Alain's Mega Charizard X or Ash-Greninja, even Sawyer's Mega Sceptile has a very good shot at taking down a Legendary Bird (Articuno-Moltres-Zapdos), based on how their strength have been depicted in the anime.
And while Tobias' Darkrai was really strong, an infamous League sweeper, it still definitely wasn't as strong as Alain's God-Tier Mega Charizard X. Mega Charizard X ploughed through 10 Mega Evolved Pokemon in a row, including an E4 ace Pokemon like Mega Houndoom. Darkrai might have swept almost an entire League (Alain's Mega Charizard X also did that BTW) but there's literally nothing to suggest that it can defeat an E4 ace Pokemon like Alain's Mega Charizard X did. In fact, Alain's Mega Charizard X was shown to be on a completely different level, it could one-shot freaking Mega Evolved Pokemon like Trevor Mega Charizard Y and Remo's Mega Garchomp like ants while in case of Darkrai even Heracross and Gible (who definitely aren't on the level of Mega Evolved Pokemon) were able to do notable chip damage on it.
Ash-Greninja did went toe-to-toe with a Mega Charizard X for a long amount of time, giving it a valiant fight lasting 8+ minutes before finally losing. It certainly didn't put up any less of a fight than Kalos E4 member's Mega Houndoom did vs Mega Charizard X....that does suggest that Ash-Greninja was well within E4 tier-range.
Plus, more importantly, Ash-Greninja was able to go toe to toe with Kalos Champion Diantha's Gardevoir, even in its Water-Veil form, troubled it throughout and forced Diantha to resort to Mega Evolution. Even after Diantha Mega Evolved her Gardevoir, Water-Veil Ash-Greninja was able to still keep up well-enough with it. And after Ash-Greninja reached its full form, it was able to thoroughly overwhelm and overpower Mega Gardevoir with Water Shuriken cutting through Shadow Ball like butter and sending Diantha's ace flying back screaming in pain, enough for Diantha to call out in concern for her Pokemon. Champions are depicted as literally invincible in the anime and Ash had been utterly destroyed by even E4 members, let alone Champions, in the past: like vs Hoenn Drake, vs Flint; also for Champions, Cynthia obliterating Paul, Trip hacked Serperior getting mauled like a joke by Alder's Bouffalant, the previous Kalos League Champion (or that's how it said like) Magnus's Absol getting obliterated without doing jack to Diantha's Gardevoir. And this tine Ash battled a freaking Champion and still, was able to put up more than just a good fight,l and even dominate the fight in the latter part. Does more than enough to suggest that Ash-Greninja belongs to the E4 level spectrum (otherwise no way a freaking Champion's ace would've had that much trouble).
How Ash-Greninja fought against Kalos Champion Diantha's Gardevoir and was able to even overpower it for a while and how long it was able to go toe to toe with Alain's God-Tier broken Mega Evolved Pokemon is more than enough to suggest that it clearly holds the title of Ash's strongest Pokemon as of now.
@Dream Lad I think that I've explained the Ash-Greninja vs Mega Gardevoir battle well-enough now. The clear difference between the examples of Pikachu vs Agatha's Gengar, Torterra vs Bertha's Hippowdon, Paul's Torterra vs Cynthia's Garchomp and Iris' Axew vs Cynthia's Garchomp is that Greninja was giving trouble to Gardevoir throughout after it transformed into Water-Veil Ash-Greninja, pressurizing Diantha enough to Mega Evolved her Gardevoir. Even after Gardevoir Mega Evolved, Ash-Greninja still was able to keep up well-enough with it and after reaching full form, was able to sheerly overpower Mega Gardevoir for a while (Water Shuriken cut through multi-fused Shadow Ball like butter) and was able to do significant amount of damage to it, enough for Diantha to call out Gardevoir's name in concern...it was a much different case than the examples you mentioned. A Pokemon which is not in the E4 tier range won't be able to give a freaking a regional Champion's ace Pokemon that much trouble. And yup the battle definitely was DBZ style with Ash-Greninja.
I agree that if Ash were to beat an E4 members someday, it'd most likely be with Pikachu starring, because it's his lifelong partner of course. I'd say that a hypothetical Mega Evolved Charizard of Ash or Pikachu in peak form with 10,000,000 Volt Thunderbolt would of course surpass Ash-Greninja in terms of strength.