The specific eye color of Edward Tudor and Tom Canty is not given in this story.  The text uses the word "eyes" a total of 85 times during the story, so it isn't as if the narrator is ignoring that facial feature.  All that readers are specifically told about Edward's eyes and Tom's eyes is that they are identical looking.  

Thou hast the same hair, the same eyes, the same voice and manner, the same form and stature, the same face and countenance that I bear. Fared we forth naked, there is none could say which was you, and which the Prince of Wales. 

I suppose it doesn't matter what color their eyes are.  The important part of the plot is not their color.  The important part of their eyes (and bodies) is that they are identical.  That's what allows the boys to exchange places.  

What I like about Twain's use of eyes in this story is that he doesn't use a character's eyes to tell readers about that character's physical form.  Twain uses eye descriptions to tell you about that character's thoughts and emotions.  For example, when a character is feeling excited or in awe, Twain tells readers that the person's eyes are "shining" or "twinkling."  There are other times when eyes are "craving" or have "burned with passion."  I think it's a really great usage of eye descriptions, because it lets the same character's eyes do so much more.  Additionally, by never telling readers what the eye color specifically is, Twain has allowed reader imagination to simply take care of that small detail.  I might think that Tom's blue eyes are twinkling, while a different reader might think that green eyes are twinkling.  Both would be received equally well by each reader because the reader is controlling the eye color.