Cooling him down is the key to helping his immune system to fight this illness. A fan blowing on him, cool wash cloths on the forehead, face and neck/chest, a mildly cool bath... all of these things will bring relief to him and will bring the fever down.
Give him cool liquids, pedialyte pops, etc.
The best home remedy, if you can give him a bath, is to put a small amount - 1/4 cup to a basin or 1 full cup to a bathtub - of apple cider vinegar in the warm/cool water. Apple cider vinegar is loaded with potassium and will give him the energy he needs to fight the flu as it is absorbed through his skin.
Bathing is super important because our skin absorbs so much of the water we are sitting in, hydrating our bodies when water cannot be ingested or when we are throwing up.
It is so easy to forget the lessons we learn from our own flu experiences when we are helping a baby ~ they seem so fragile! Think of your own flu experiences - wrap his body but cool his face if he wants covers. Don't wrap him if he doesn't.
Never leave him alone while his fever is high, but don't forget the easiest tools you have to help that fever to come down. You won't sleep while he's sick, but you will be glad he got through it safely and without antibiotics - which can mask a child's symptoms and lull you into a sense of safety that could be dangerous.
Once his fever breaks he will be feeling better, but still be vulnerable for two-three days following. Keep him immune system on the offensive by giving him more baths, but making them warmer so that he stays warm.
The dance of the flu is not hard once you get it down. He will have the flu many times in his life - shots or not. The best response is to dance - apply cold when he is hot - hot when he is cold.