My manager's going to Anne Frank's house on Monday - he was looking at buying a ticket in advance, but they're only available from mid-June, looking now. I went when it opened at 9am, and I had to wait about 20 minutes to get in; when I came out, the queue was far longer, at least 2 hours, so plan to go early or late in the day, unless you've got tickets in advance. I think you need to have read the Diary and/or have some understanding of why they were in hiding and later in concentration camps to really get it, and I don't know that I'd take children much under secondary age.
The zoo is popular too, as well as the science museum. The Rijksmuseum has things I would have adored as a child, and still enjoyed as an adult, including a large model ship and the dollshouses. I'd have sold my parents (well, at least my sister) for a dollshouse like that when I was a child! Beautiful model houses and furnishings (for adults, rather than children.) I did enjoy the Van Gogh museum, but I'm not sure I'd have been so keen as a child - however, I wasn't so keen on Van Gogh.
If you're there for a few days, it might be worth getting the train out to the Zaanstreek and seeing the windmills there - it's not a long journey, and there are a number of working mills.
I'd avoid the red light district - I wasn't paying too much attention as I was wandering round the streets in the morning, and just ended up there, and I was half way along before I realised, but I think later in the day, it would be more obvious (and I still wonder why anyone would think a single woman on a sunny, dry spring morning would want to go in to watch a live sex show, but at least they are not sexist, in that they call out to everyone passing...) Round the Leidseplein in the evening, it's lots of sports bars and Argentinian steak houses, and I wouldn't bother, other than to marvel at the number of steak houses. How much steak can any population eat? But there is so much else to see and do, it's easy to avoid the bits you'd rather not do with children, especially if you pay a bit more attention to where you're walking than I did.
I think I need to persuade my Dutch colleagues I need a week in the office there...