Hi!
Chiming in from Eastern Prince William County (I work in DC also).
If I could afford it, I would choose Fairfax County. Overall, the schools have a nudge over Prince William County (but not ALL the schools) and I think, in general, living in Fairfax is pretty nice albeit congested. My favorite areas are probably Burke, Fairfax, Vienna, Oakton. For a cheaper area in Fairfax, parts of Springfield and Lorton are also good.
I've lived in Vienna/Oakton and Fairfax since 1994. Love it here. The traffic can be overbearing, BUT there are ways around that. It IS expensive. But you have some of the best amenities offered around. Schools, libraries, recreation availability, youth sports.
Having said that, I really don't mind Prince William County and there are things about Prince Williams County that I prefer over much of Fairfax. To me, it just doesn't seem as packed as Fairfax. At any given time, the Woodbridge Wegman's is much less congested than the Fairfax Wegman's (popular grocery store chain if you are unfamiliar with it). Absolutely true. Our fairfax Wegmans is always packed, although they do staff it well.In Woodbridge (the town I'm in), the didn't build every shopping center off in one single area so I find it pretty easy to navigate around Woodbridge. When I'm in Fairfax, I often find myself creeping along thorougfares on the weekends because the roads just can't accommodate the people there.
In my end of the county, we have some of the BEST public transit options. There is the PRTC Omnilink bus service right into DC using HOV lanes, there is the VRE train (probably the least favorite option), and then there are the slug lines which are fantastic and I have used them frequently. The Western end of the county doesn't seem to have all that available or, at least not to the degree we do here but that part of the county is "younger" as far as development. West of the city has much of that, with the exception of the slug lines. I'm a HOV exempt commuter, so my commute is bearable.The VRE sounds like an attractive option but it really depends on where you work in DC as to how convenient it is. Some people work near the last VRE stop and that's great. Others have to get off the VRE and move over to the Metro subway system to complete their ride. I know that my coworker, who lives in Manassas, VA, takes the VRE but it is at least an hour and a half commute for him when he factors his walk to the VRE, the actual train ride, his transfer and ride on Metro, and then his walk to his workplace.
A lot of people choose Prince William County so they can get more real estate, and you will get that here, but there are tradeoffs. Right now your kids are pretty young and most, if not all, elementary schools in both counties are great. It is the middle schools where things can suffer.
But, to repeat, if I had to do it again, I would choose Fairfax for the school system.
I was amazed at how quickly middle school crept up on me (and in most of fairfax, it starts in 7th, not 6th grade, which I think is a plus). There are questionable middle schools in Fairfax, there's one that you may go to if you live in Vienna, but where I am, all three local middle schools are wonderful according to parents and kids.