Though not necessarily kid-oriented, they may enjoy the boat rides on one of the lakes in the area: Starnberger See, Amersee or Tegernsee.
Those are very lively places, when the weather is nice you can even go to the "beach", go to nice outdoor cafes, ice-cream parlors, etc.

If the weather is bad, the Deutsches Museum is great idea... it has some sort of planetarium on the rooftop and an Imax nearby, if you kids are not "that" into musems...