In my eyes = there is something (physically) in my eyes ' I have sand in my eyes' however I can't think of a situation where I would use 'on' my eyes - perhaps using face cream on my eyelids (not on my eyes).
' In my eyes' sounds like a poor translation of ' à mon avis', as I see it, in my opinion.
Hope this helps
Also you can use that expression as a figurative speech, for example: I can't change that idea, they're innocent in my eyes. for you they look innocent, be it like that or not.