If someone told me I had 'nice eyes' I would be flattered because it's a pleasant thing to be told. Over and above that, I would be quite pleased, because 'reading eyes' is one of those neurotypical things that means a lot in standard social intercourse. I would instinctively tend to react warmly to a comment like that, even though I would hesitate to give a standardised response to it. I think a responsive smile and a "Thank you!" would be appropriate, and see where you go from there, because it certainly indicates a level of interpersonal connection.