We have done both.
Are you traveling with little kids? If so, I'd say Chocolate Kingdom is your best bet. The tour features a cartoon dragon that helps tell the story of how chocolate is made. There is an option to add on a make-your-own chocolate bar at the end, which was also a nice compliment to the rest of the experience.
The Chocolate Museum and Cafe has a more grown-up feel vs. Chocolate Kingdom. They have some really fabulous sculptures made from chocolate that are super impressive. Their wine and chocolate tasting is really quite enjoyable .... was a great pairing (pun intended) to the tour.
Not to say the Museum and Cafe isn't "kid friendly", but Chocolate Kingdom is definitely moreso.