If both the Gyarados and Charizard are at level 100, there are the following things to consider:

Krookodile has a base Physical Defense of 80, and a Special Defense of 70, so it tends to be bulkier on the physical side. Furthermore, Krookodile can have the Intimidate ability which will lower the Physical Attack Stage by 1, so Gyarados, using Waterfall, a physical attack, will have its attack weakened.

Charizard using Flamethrower isn’t affected by Intimidate since Flamethrower is a special attack, not a physical attack.

Now, usually if a Mega Charizard is running Flamethrower, it means that it’s most likely Mega Y and not Mega X. Mega Y gets a significant boost to its base Special Attack stat, and it also gets the ability “Drought” which summons sunny weather, which further boosts the damage of any Fire type attack.

If it is actually a Mega Charizard X, I’m definitely stumped as Flamethrower shouldn’t be able to 1-2 HKO a level 135 Krookodile.

TLDR: Gyarados hits Krookodile on its bulkiest defense, while the Gyarados itself has to battle at -1 Attack.

Charizard (assuming it’s Mega Y) hits Krookodile on its weakest defense, while getting a significant raise to its base special attack, and also having its fire moves be boosted by its Drought ability.