Migrate> Poke Transporter> Pokémon Bank> PKMN Y/ ORAS
Basically, there's no other way.
If you wish to transfer your Rayquaza from whichever game you have you must do it that order.
Gen 3 ( Ruby, Sapphire, Emerald) to Gen 4 (Pearl, Diamond, Platinum)
Gen 4 to Gen 5 (Black, White, White 2, Black 2)
Poke Transporter to Pokémon Bank to Y or ORAS