Hi there! You will love the Netherlands! I lived there in 2010 for 5 months but missed tulip season so I went back in 2015 specifically to see the tulips and I will never forget the beauty! For Kukenhof: My suggestion is to get there right when it opens (I believe 8AM) and you will have the place to yourself for 20-30 minutes until the tour buses arrive. Bring your camera! 2-3 hours there is probably enough. If you have a rental car, drive around the bulb region and just allow yourself to get lost. This was my favorite part of my trip...it's beautiful! You can pull over and get out and see the flowers at your leisure.
If you're going to be in Amsterdam, the Van Gough Museum and Rijksmuseum are my favorite! Your son will love the canal ride as well! The Anne Frank House is a bit crowded and dark inside so if he's able to do all of these activities, great, but you may want to miss one of the museums and just go for a walk in Dam Square or Vondel Park to let him wander around :) Don't forget to get a Dutch pancake (your son will love it!).
Harleem is a big city that I didn't spend too much time in, but if you have time and are traveling by car (or train but I'm not sure how close the station is) I would suggest visiting Zaanse Schans. It's touristy, but it's fun to see the working windmills and the little city. They have windmills that you can go inside and see how they work and shops where you can taste some wonderful gouda cheese. Hope this helps! The Netherlands is one of my favorite places in the world!
If you happen to go south...stop in 's-Hertogenbosch for a bosch bollen - you will NOT be disappointed :) p.s. plan on rain...it always rains!