You said this is an annual trip, but didn't say which NPs you have already visited. Have you been to the Smokies, Mammoth Cave, Shenandoah, and Natchez Trace and Blue Ridge Parkways?
As others have said, if you can fly, our sons still remember a boyhood trip to Yellowstone. It had the geysers, hot pools, mudpots, paintpots, and Yellowstone Lake, of course, but also had more wildlife than they had ever seen.
When our youngest son was 6, we went to Yellowstone Falls very early one morning. We were the first car in the parking lot and there were buffalo grazing on the parking lot landscape strips. We parked, stayed quietly in the car, and watched adult buffalo walk right around the car to get to the other side of the parking lot. We waited until they were completely out of sight, then ventured to the overlook for the falls. The falls are spectacular, but the proximity and size of the buffalo were the primary topic of conversation among the boys for the remainder of the trip!
If you have to drive, you might be able to get to the Black Hills and back in a week. You can go to Mt. Rushmore, then Wind Cave National Park for a view of the buffalo and elk herds there. The giant faces, the cave, and the buffalo should leave your son with some lasting memories.
You can also drive through the Badlands NP on the way there or back just to check it off your list, but there may not be much of interest there to a 6 year-old. And, if you had more time, I would highly recommending spending time in Custer State Park, which also has a buffalo herd, fishing lakes, and great drives through some very narrow tunnels. There is also a steam train that your son might enjoy that runs from Hill City to Keystone (Google "1880 Train").