Kyogre is the strongest Water-type in Pokemon Go, potentially for all time. The biggest threat to Kyogre's throne is none other than Kyogre itself - either with a non-TMable Origin Pulse, or a separate Primal Form. Kyogre Candy is therefore extremely valuable; whenever Kyogre resurfaces in Raids, you should prioritize raiding it as much as you realistically can. As always, raiding in groups of 5 or fewer is essential for maximizing rewards out of each Premium Raid Pass.
After the 20% HP buff in February 2019, the Kyogre duo is now borderline impossible. With Rainy Weather, Best Friends, and against the easiest moveset (Waterfall/Thunder), Level 40 Raikou has a TTW of 601.2 seconds, with 24 deaths. Theoretically, there is an extremely small chance to pull off the Rainy duo with incredible RNG, but for the most part this is impractical. This guide will therefore focus on the trio, which is much easier.
Minimum viable levels assume Best Friends, No Weather.
Italics indicate a Legacy move.
The viable counters for Thunder and Hydro Pump are mostly identical. The most notable difference is that Electivire is significantly less viable against Hydro Pump, due to how frail it is. Hydro Pump will OHKO Electivire after 2 Waterfalls if not dodged, even at Level 40.
Against Blizzard, Grass-types are non-viable due to being OHKO'd every few seconds. The list of viable counters therefore consists solely of the top-tier Electric-types.