Claydol would make a great counter to Aura Sphere / Extra Sensory / T-bolt / Calm Mind Raikou. Immune to STAB, STAB EQ, Strong Defenses, and resists both moves.
Raikou's Aura Sphere when super Effective is the same damage output as Thunder when neutral. So really, its probably better to just use Rain Dance/Calm Mind, Thunder, Weather Ball, Extrasensory/Hidden Power Ice.
(If using CM, then have a Damp Water Rain Dance user).
And to counter that set, Lanturn works well, especially those that carry Toxic, and Stockpile. Torterra counters the Non-Hp Ice Variants, as it can Rock Polish on an CALM MIND Aura Sphere and then proceed to sweep.
In OU Latias can counter the Extrasensory/Thunderbolt/Aura Sphere/Calm Mind version, while Hippowdon can probably counter the Rain Dance Version since it makes Weatherball Rock which it resists, is Immune to Thunder/bolt, and if Raikou is carrying Aura Sphere over HP Ice, then it is forced to switch. If Raikou is carrying Hidden Power Ice over Aura Sphere then Swampert can also be a good check.
Electivire makes a good check, similar to Dugtrio, if it switches into Thunder/bolt, and can threat back with a Life Orb EQ.