We have done it both ways. Staying in Massanutten and driving to the metro station, and taking the Massanutten tour. We also live close enough that we have been there on our own - staying at a hotel outside the city, and our kids went on field trips from school for the day which I chaperoned a few times.
We REALLY enjoyed the Massanutten tour for a few reasons. They do the driving, they brought us places we have wanted to see but never got around to (Arlington comes to mind), we didnt have to deal with the metro (which actually is NOT that bad) and most of all -after the long day it was nice to get on the bus and close our eyes!! The tour bus stopped at Golden Corral on the way back to Mass.
So when it is just the 2 of us, we would definately take the tour again. We saw more in the one day bus trip than we could possibly have seen on our own. When we bring kids/grandkids then we drive to the metro.
You could take the tour in and see a quick view of the city, if you want to go back and spend more time - do the drive in another day.