The best moveset would still be the one that was named in Generation 3.
Item: Wise Glasses
EVs: 252 Sp. Atk, 128 Spd, 128 Sp. Def
Firstly, Calm Mind to raise Sp. Atk for the other three moves. It also raises Sp. Def for some protection from most Grass and Electric attacks.
Surf is STAB. Considering Sp. Atk is maxed out, the item is wise glasses, and Calm Mind is used, this attack does a hell lot of damage.
Ice Beam is another strong move to get rid of the danger of Grass types. It'll also help against Dragon types, which might know an Electric move.
Thunder is a stronger version of Thunderbolt. And considering Kyogre's ability is Drizzle, Thunder won't miss because of the rain. It's a strong move and is especially useful for other Water types, who may use Drizzle to their advantage.