Ok, given that you have three main gods of Greek mythology, you could model them off of the Kami trio if you wanted, and make them humanoid. Or, you could just go by animals or concepts that the Gods themselves represent.
Hades - Fire/Dark - Think the Balrog from the Lord of The Rings, The Three headed Dog Cerberus, or like a 'grim reaper' archetype.
Zeus - Electric/Flying - Zeus often took the form of an eagle or bull, and was the Sky God who wielded the famous Lightning bolt. Tauros/Braviary + Zapdos?
Poseidon - Water - Any kind of large fish or sea creature, really - Dolphins, especially. Could kind of conflict with Kyogre, though.