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if you look at the code, they're already cropping a roi for the faces:

 roi_color = img[y:y+h, x:x+w]

now you'll do the same, just for the eyes:

# global var:
eye_counter = 0

        eyes = eye_cascade.detectMultiScale(roi_gray)
        for (ex,ey,ew,eh) in eyes:
            # here's your eye-roi, see, it's the very same pattern
            roi_color_eye = roi_color[ey:ey+eh, ex:ex+ew]
            # write image *before* drawing stuff on it
            cv2.imwrite("eye_%d.png" % eye_counter, roi_color_eye)
            eye_counter += 1
            cv2.rectangle(roi_color,(ex,ey),(ex+ew,ey+eh),(0,255,0),2)