Why are you trying to steer clear of Norfolk? Norfolk is awesome and has some wonderful, family friendly neighborhoods. We have lived in Norfolk for a total of 7 years of DH's career and I LOVE it here. We PCS next week and I have been boo-hooing all day. You just need to be careful about picking your neighborhood carefully, but you can't beat the shopping, restaurants, and charm of Norfolk. I just love it. We live in Larchmont (a neighborhood in Norfolk), but there are several others that are really great.
As for Williamsburg, I went to graduate school at William & Mary so I am familiar with it. W'Burg is a charming place with some great things going for it. The cost of living is very slightly lower than Hampton Roads. There are some very cute neighborhoods and apartments. The shopping is decent and there are good outlets. James City County has good schools which is a perk if you have kids.
The cons: It is super touristy and that corridor can be tough when it comes to traffic. The commute to Newport News wouldnt' be too bad (and honestly, I wouldn't blame you for living in W'Burg if you were 100% confident your DH's tour was going to stay in the shipyards). However, if you do have even the slightest worry about his job moving to Norfolk I think W'Burg would be tough. I commuted from our home in Norfolk to Williamsburg almost daily for graduate school and it was ROUGH. I had no kids and DH was deployed a good portion of my time at school, so I didn't really care about the time I spent on I 64. But now with a few kids I would not want that kind of commute daily.
Overall - W'Burg is really cute and nice. But please don't "steer clear" of Norfolk because you think it is a bad city. Norfolk truly is a great town. You just need to educate yourself. (just like you would with VA Beach, Chesapeake, or any other HR town).