Not sure if you dealt with it, but it could also be part of the acid reflux. When we needed to up dosage for my daughter, we had her waking up out of her normal schedule hacking, snoring, and coughing. Once we upped her meds it has gotten better.
It has been a few days since you posted your question, so I do hope that you did take your baby to see the doctor.
If not, then make an appointment and get baby checked out. It sounds that he may have a chest infection and may require an antibiotic.
You can buy Vick that is suitable for young children and vapour plugs that you plug into a socket that give off menthol vapours.
You can also put in a corner of the room a bowl of hot water with some Vick in it so as to allow the steam vapours into the room to help him breathe. If you do have other children, do make sure that they cannot reach the bowl of water.
Keep the baby warm and offer a warm diluted baby juice drink or just plain water.
The doctor may also prescribe a baby pain relief medication in suspension form to help reduce any raised temperature.
Best wishes.