I found Kyogre very easy to catch without a Master Ball... took me a mere 2 Ultra Balls. Helps to have a squad in the mid 40's for easy capture. Try to avoid picking on the water weakness (although if it uses Calm Mind enough, that may be your only way to bring it's health down). Once in the red, just keep throwing those Ultra Balls, it's not actually that bad. Have something in your squad that can resist Ice and Water (a good Water type works for both, I used my Lombre (bad move with the Ice, I know) ) and watch out for Body Slam's paralysis. Apart from that, it should be a breeze...
If you want the Master Ball, however, you find it in Team Aqua's base. There's an area with 4 item balls on the ground.. one of those is a Nugget, one is the Master Ball, and the other 2 are L30 Electrodes. If you're past that and have missed the Master Ball, then you've got no chance of getting it unless you reset and start again, or win the Lotto at Lilycove. Odds of matching all 5 numbers are 1 in 100,000, divided by the different ID numbers in your pokemon squad. Good luck :-)