I caught Rayquaza with an Ultra ball on level 70 in the Sky Pillar. It is very hard to catch. I reccomend that you save the game before battleing Rayquaza so if you accidently kill it or if it kills you you can shut the game off and turn it back on so you can try to catch it again. Same thing for Kyogre who is in Cave of Origin. So you never run out of tries.

Note:You need to beat the champion before catching Rayquaza.