Due to the way perspective works the larger eye should be the one closer to the camera and the smaller eye should be the one further away. Usually.
Things that are of equal size look larger when they are closer and smaller when they are further away. Our brains expect that when we view a person from an angle the eye further away from us will appear smaller than the eye closer to us. If, by turning your subject's head, you can only create enough difference in distance to make them both the same size in terms of their width on the sensor, the viewers brain will still see that there is something odd going on.
By keeping the smaller eye further from the camera and the larger eye closer to the camera it satisfies the viewer's expectation that the nearer object will appear larger than the more distant one.