I have a video from Jack Nicklaus discussing short game and in it, at about 15:43 he talks about having " eyes over the ball. ...down the line over the ball" for putting.
I feel more comfortable my eyes along the target line to the hole but sometimes I feel the ball more comfortable place when the ball is so that my eyes are slightly inside not directly over the ball. This is especially true for me in longer putts. However for shorter putts eyes directly over the ball-target line works too.
Im not sure which method is better. I tend to slightly "cut stroke" my longer putts and "draw stroke" my shorter ones.