The only way to change your avi's base eye color is to delete your base. This will not delete any of your items, however, if you've purchased hair from the Durem Salon and it's not one of the starter choices, you'll have to repurchase that. You'll also lose any special skin you might have, like dark elf skin. It's recreating you whole avatar over like when you joined.
The link can be found under Account Settings: Preferences then under the paragraph about gender changes. Or
here.
There are also numerous items on Gaia that have contacts that layer over your eyes. Some, like the oculus mythica, have only eye poses but many others have a single contact pose mixed in with all the rest.