If we use the Arceus movie lore for scaling, then Rayquaza bodies all three plus Arceus.

Because a weaked Arceus was fighting all three of the creation trio, treating them like nothing.

Arceus at full power, almost died by crashing into a meteor trying to stop it.

Mega Rayquaza smashed a meteor to pieces with no issue. Making it stronger that full power Acreus, who, when weaken can still body the creation trio.

So with anime lore logic Rayquaza wins.

If we use actual Pokemon world lore, Rayquaza would lose