Credit goes to Gibbed
First download the latest Gibbed Mass Effect 3 editor from here: http://svn.gib.me/builds/masseffect3/
NOTE: You cannnot do this with the pre made Shepard.
Next follow this tutorial created by Gibbed
Remove the "" if you are copying and pasting.
TIM eyes guide for ME3:
Extract your Save_000# file out of ur save and open it in Gibbeds mass effect 3 editor
1) In Raw -> Player -> Appearance -> Morph Head...
2) Open TextureParameters...
3) If there is an entry named "EYE_Diff", remove it.
4) If there is an entry named "EYE_Spec", remove it.
5) Add a new entry, name "EYE_Diff", value "BIOG_HMM_HED_PROMorph.IllusiveMan.HMM_HED_PROIllu siveman_Eye_Diff"
6) Add a new entry, name "EYE_Spec", value "BIOG_HMM_HED_PROMorph.IllusiveMan.HMM_HED_PROIllu siveman_Eye_Spec"
7) Click OK.
8) Open VectorParameters...
9) If there is an entry named "EYE_Iris_Colour_Vector", remove it.
10) If there is an entry named "EYE_Iris_Spec_Colour", remove it.
11) If there is an entry named "Emis_Color", remove it.
12) Add new entry, name "EYE_Iris_Colour_Vector":
R "0.008373"
G "0.505433"
B "0.867136"
A "1"
13) Add new entry, name "EYE_Iris_Spec_Colour"
R "0.2"
G "0.2"
B "0.2"
A "0"
14) Add new entry, name "Emis_Color"
R "0.160444"
G "1"
B "1"
A "1"
15) Click OK.
16) Save, play... etc.
If you don't like the color that your eyes come out to be then simply change the RGB of Emis_Color, Eye_Iris_Color and Eye_Spec_Color