These are 2 different locations which are 1.6km apart from another. That´s 4 minutes by car.
The VW Museum is a museum as you can tell by the name
At the Autostadt you can pick up your new car right after production. If you buy a new car at the dealer you can also book a day at the Autostadt with lots of events all about VW and its history and stuff that has to do with cars and VW. After a tour through the Autostadt you can pick up your brand new car and drive home with it instead of having it transported to your dealership.