Rayquaza is level 35. Try teaching Mudkip Ice Beam and teach Bulbasaur Bullet Seed. Those two are powerful moves that can KO Rayquaza in a few hits. If you don't have those TMs, then you can go here and request for it: http://www.serebiiforums.com/showthread.php?t=165109
They will give you a password. Enter that password in the option "Wonder Mail" under the main menu.