Kyogre's strongest moves:
Water Spout - Base Power 150(via level up at level 90)
Hyper Beam - Base Power 150(via TM)
Giga Impact - Base Power 150(via TM)
[Source][1]
Groudon's strongest moves:
Eruption - Base Power 150(via level up at level 90)
Hyper Beam - Base Power 150(via TM)
Giga Impact - Base Power 150(via TM)
[Source][2]
Edit from Blob
Must note that when stab is taken into account Water Spout hits 225 base power. Groudon does not get this same boost for Eruption given it is a Ground not Fire type. Groudon does however learn Earthquake which after stab hits a 150BP which is a good alternative to Giga Impact as no turn recharge is required after use.
When taking the rain and sun taken into play (summoned by each Pokemon), Eruption and Water Spout are further increased by 50%.
[1]: http://pokemondb.net/pokedex/kyogre
[2]: http://pokemondb.net/pokedex/groudon