Rayquaza: After you have gone to Sky Pillar once and called Rayquaza to Sootopolis City, you can get a lvl 70 Rayquaza by returning to Sky Pillar.
Kyogre: After finishing the Pokémon League, go to the person in the Weather Institute who gave you Castform and talk to him. He will tell you there is very heavy rain on some route (it can be one of several). You must dive in one of the dive marks in that area. Go till the end and there will be a cave called Marine Cave. In the end of the cave there will be a lvl 70 Kyogre.
Groudon: Go to the guy in the Weather Institute and talk to him. He will say there is bright sunlight in one area. Go to the area, and there will be a cave called Terra Cave. There will be a lvl 70 Groudon waiting for you.
Kyogre and Groudon are active at different times and neither necessarily comes first, so you may end up going for Groudon first.
Rayquaza is found before the E4 while Groudon and Kyogre are postgame.