My boys were getting over colds when they got their seasonal flu shots. The nurse said as long as they didn't have fevers & didn't have any severe symptoms, they would be fine.
Especially since your son will be getting the inactivated vaccine (as opposed to FluMist which is the live vaccine), I wouldn't worry too much as long as he doesn't have a fever and isn't acting markedly 'sick.' Part of my feeling is based on the fact that the h1n1 vaccine has not been in very high supply yet, esp. the shot version- since you have the chance to do it now I might not be inclined to wait long and risk them running out.