My kids LOVE the National Aquarium in Baltimore. We go at least a few times each year. Its so relaxing and serene inside. Also, there is a wonderful dolphin show - don't miss it!
There are plenty of other things for kids to do in that area. There is the ESPN club, and Port Discovery, and all sorts of little shops to browse through. There are great restaurants, and also a nice eatery with lots of different selections. On most weekends you can find outdoor entertainment - sometimes a juggler or a mime or some such. Always a good time, we love the Aquarium/Inner Harbor and I think your 6 year old will too.