I would talk to the pediatrician to see if there is an infant-approved nasal spray and to make sure there is nothing more than a runny nose. Also, plan to nurse/bottle feed/pacify during take offs and as you feel the plane start to change pressure/altitude prior to landing (it may be awhile before). If your son is sleeping, I wouldn't wake him, babies seem to handle the pressure changes quite well while asleep. Do NOT hold off on feeding a hungry baby to make sure he'll drink when he needs to, a hysterical child is far harder to soothe than a content one.
Look for a product called "earplanes" in the drug store, they are rubber ear plugs that aid in ear pressure relief for flying. They come in different sizes, I'm not sure what the youngest age is. My daughter (6 yo) just flew with a head cold with 3 stopovers and these helped immensely!
And finally, here is a flight attendant method for ear relief, but it is dangerous so they do not like to help you. Get a cup of hot water, a paper towel and a spare cup from the flight attendant. Wet the papertowel with the hot water and put it in the empty cup, hold the cup with the hot towel against your sons head with the ear in the cup, this will help relieve the pressure. It is dangerous because hot water from the paper towel can burn your child, if you are desperate and have cooperative flight attendants, they may let you do this.