First place to start would be to pick your rainmaker, though you only have 3 choices: Politoed, Pelipper, and Kyogre. Kyogre is banned in a lot of formats though so it's safer to go with the frog or the bird.
From there you can start picking out the rest of the team. Stuff that benefits from the rain is obviously what you want to pick. Mega Swampert makes for a pretty nice rain sweeper, so I'd recommend that. Electric, Grass, and Steel types are a common sight on rain teams since Electric types get 100% accuracy Thunder in the rain and can potentially beat a lot of the Water types on the opposing team that might try to tank your Water types, while Grass and Steel types like it that Fire is less effective while the rain is up.
What are you playing on btw, 3DS or Showdown? And singles or doubles?