RACHEL: Do you wear contacts?
LORELAI: Me? No.
RACHEL: God, you’ve got amazing eyes.
In the Pilot, Lorelai complained that she felt as if she’d put her contact lenses in backwards, so she does actually wear contacts, and there are numerous references to her wearing either glasses or contacts throughout the series. Maybe Lorelai assumed Rachel meant coloured contact lenses, thinking her eyes were too blue to be natural (and her assumption may have been correct, as wearing normal contacts doesn’t give the wearer “amazing eyes”, just improved vision).