Here is what I did. First get an Umbreon with Mean look and Taunt. Find Raikou then use Mean-look to make him not run, then use Taunt so he can not use Roar to escape. Then lower Raikou's HP down until it is low enough to throw balls at, I reccomend using it at night with Dusk-balls.
If you can, have Umbreon know Baton-pass then you can use it after using Mean look and Taunt to a Pokemon with False-swipe and Taunt to make an easier capture.