I'm Dutch and live here, my best tips would be:
The Hague beach go to Kijkduin, or any of other beaches but Scheveningen, it's a nightmare with parking and it's just not a very nice beach, very commercial and busy. There's a sea life but it's a bit crap. Wassenaarse slag (near Duinrell) if you just want a nice beach in the midst of beautiful dunes. There's a lot of infrastructure projects happening in The Hague city centre currently and they'll continue on long term and it includes a lot of the sight seeing places so unless you want to see something specific I'd avoid the city centre and head to Museon instead which is an educational children's museum and there's an IMAX theatre (Omniversum) showing nature documentaries next to it, not very far from Madurodam. Across the road from Museon is the prime Minister's residence (he doesn't live there), Het Catshuis, where you can have a peak through the gates. The nearby Frederik Hendriklaan is a sort of posh high street, good for a coffee, specialty groceries, etc. it's also expat central and there's a nice communal green and playground. When leaving the city you can stop by Huis ten Bosch, again to peak through the gates of where the royal family lives.
If your boys are into curious/sciency things I'd definitely recommend the Teyler's Museum in Haarlem (great little town outside of Amsterdam, have some fries at Friet Hoes, you could potentially park and train into Amsterdam from here, nearby Bloemendaal beach is also lovely), it's a really interesting building and originally a curiosity cabinet and children seem to love it. If you plan on going to several museums get an annual Museumkaart, Nemo in Amsterdam is a definite one to visit with children as is Naturalis near Leiden and the Maritime museum in Rotterdam is a good bet too, and they have a child specific museum in Villa Zebra.
Dordrecht is an amazing little historic city centre that often gets overlooked by tourists. Not too far from Kinderdijk if you're heading there. You can go there by public transport boat from Rotterdam as well (or take the boat into Rotterdam, it's really impressive to see it from the water), I'd suggest stopping off for lunch in Villa Augustus, an old water tower converted into a hotel with a huge vegetable garden that supplies the restaurant. It's very family friendly.
I'd also suggest keeping an eye on www.spoordeelwinkel.nl it's where the train operator hosts special offers from any station in the Netherlands and it's often in combination with attractions, like a canal tour in Amsterdam.
If you want to go out and see the flowers, Keukenhof is the traditional place to go to (have some poffertjes while you're there). There's also some official fields to visit now as tourists and their Instagram pictures were a bit of a nuisance, check with the Lisse VVV (tourist information). Nearby (and probably not far from where you're staying) is Landgoed de Olmenhorst, you can pick apples (bring wellies), there's a farm shop, cafe, etc and they usually have a lot of activities for children going on, especially in the holiday period, but even if you're there on a quiet day, there's always a scavenger hunt available.
Giethoorn is a bit farther out, a sort of Dutch Venice. I've personally never been but any visiting friends who have been can't stop gushing about it 🤷
I personally love visiting Maastricht but it's very far (somewhat closer to Efteling), it feels very different to the rest of NL.