Is he breast or bottle fed? If he's breastfed, you could try offering just one side at the 3am feed and then the other side when he wakes for the day. Dd3 used to wake between 3-5am and I did that with her and she was still ready for a top up in the morning and then I would count my E's from there.
If he's bottle fed, I would probably reduce the size of the amount, again, so that he's ready for more when he wakes for the day
Hth