Route 14, where you can catch them. It rains frequently there. I have seen rain in many locations tough, so it seems pretty random. The postgame city is a good place as well, tough the only battle to abuse it with is the daily rival battle.
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If you want to have an easier time with it, just carry a rare candy and start flying between some cities where it rains. I know Kiloude City seems to have some kind of monsoon going on half the time I go to check my new hatches' IVs.
The swamp rains often. Fly to north luminose exit up and walk up abit. If it's not raining yet, fly to the fairy gym town and walk to the swamp. Rinse/Repeat til it rains. Shouldn't take too long... Unless you've been to kiloude then go there instead - I heard it rains there a lot. I've played for 60hrs and only just got Xerneas.