Amsterdam after dark is fine for the mst part. I wouldn't ride the metro alone, nor would i visit the RLD and surrounds after dark, but I assume with two young boys the RLD is not on the menu. The centre is fine and very busy. You just need to take the usual precautions.
If jetlag isn't a problem then Madurodam is doable, I'm sure your boys will like it. You could combine it with wandering around Den Haag - visit the pariament buildings, the royal palaces, and as I said Panorama Mesdag - that is something yu all will enjoy.

Thanks.