Please, please factor in the length of commute time for your husband as a very high priority in whatever choice you make. If he and you are not used to his having a long commute -- you need to either be prepared for that to be part of your life or to make compromises on your son's schooling, costs of living etc., in order to avoid a long commute. A long commute is fine with some families; for others, it would mean he would not be there to help take your son to school or extracurricular events, he would not be home until late some evenings, you will see less of him, etc. I suspect you are not currently used to your husband taking a hour or more each way to get to and from work, and you can expect that to change dramatically when you get here. Unfortunately you do not want to live in SE DC or in the Maryland areas bordering SE DC, due to crime and poor education issues, so accept that your husband WILL have a commute (whether by car, Metro, rail, carpool, whatever) wherever you live.
Chantilly, Reston etc. are great places but way, way too far to commute to a job in SE DC, I think. Stafford is possible but that puts you down south along I-95 and that is a totally unpredictable commute if he drives. Virginia Railway Express as someone mentioned is doable from Stafford, BUT depends on whether he has a VRE station anywhere near his workplace, whether he needs a car during the work day, how long it would take him to get to VRE from your home, whether he would have very early or very late hours (VRE is not 24 hours) and so on.
I would definitely visit this area first before you make any commitments on where to live. When you say you've "looked at" Fairfax County and Stafford, do you mean you've actually visited, driven around, tried a rush-hour drive to his work location -- or you've just considered those areas but not visited them in person? I would come up here immediately and do a lot of driving here during the most crushing hours for commutes (if those are his workign hours) and see what it's realistically like.
You also need to do a lot of research on school systems. Fairfax has an excellent county school system and so does Arlington County ( the latter has a ton of money and a relatively low number of students so it offers a lot that other school systems can't). Personally with a commute to SE I would look harder at Arlington rather than Stafford or Fairfax, though I live in Fairfax and like it a lot. Arlington is both a city and a county -- it is officially a county but is pretty much a self-contained small city. It will have a higher cost of living than Stafford but also has some older housing that might either be just right for you or might put you off since some houses are small, but the school system's reputation is good and the location is much better to get to SE DC than if you are in Fairfax County, I would think.