Bulbapedia has all 3 colors listed as his eye color, his official artworks make him look like he has gray eyes, the opening coronation thingy in the Black and White games show him with blue eyes, and I have no idea where them being green comes from. Since they are shown to be blue in the coronation thing, that's the color I'm going with, but I'm still not sure its right...
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Pokécharms
Midnight Heart
TooBlue12
I say just draw whichever you think looks best.