I used to take school trips to London and I've done loads of independent trips with kids, so here are my thoughts:
1. Madame Tussaud's???
No! no! no! Being dragged around a place filled with wax effigies of people you've largely never heard of is definitely NOT a fun day out for kids! I've never understood why people take their kids there. Avoid!
2. I note that the Tower of London has been suggested above. In my opinion it's vastly overpriced and extremely BORING!
3. The Science Museum is undoubtedly the best place to take youngsters in London. It's massive, so you need to be selective about what you look at. (The aeronautics and space sections are well worth a visit). However the star attraction is undoubtedly the interactive section. Unlike most of the rest of the museum, you have to pay for entry (with booking tickets online highly recommended) but it's TOTALLY UNMISSABLE!
https://www.sciencemuseum.org.uk/see-and-do/wonderlab-equinor-gallery
4. I see that the Natural History Museum has been suggested above. It's right next door to the Science Museum, so the two can easily be paired together but it's definitely a place where you need to be selective with regard to the galleries that you visit and also what you choose to look at within those galleries. (Much of the Natural History Museum is totally boring for youngsters). For example, the dinosaurs gallery might sound inviting but a lot of it is filled with boring display cases filled with fragments of teeth and bones. However if you bypass those and go straight to the end of the gallery, you'll encounter a moving, roaring Tyrannosaurus Rex - now that IS fun for kids!
https://www.nhm.ac.uk/visit/galleries-and-museum-map/dinosaurs.html
5. The V&A is just across the road from the Science Museum and the Natural History Museum. Much of it would be of little interest to kids but there might be a few galleries or activities that would merit a look:
https://www.vam.ac.uk/whatson/programmes/family
6. A river trip can be fun as long as you keep it SHORT. (Kids get bored very quickly on boats!). Avoid the mega-expensive tour boats though. Just use the river bus services. (The crew provide a 'free' commentary and then hold their hands out for a tip when you get off).
So I suggest leaving the coach at Embankment. Then join an eastbound river bus service at either Westminster Pier or Embankment Pier for the short journey up to Tower Pier. That takes in lots of the sites, such as the Houses of Parliament, Cleopatra's Needle, the London Monument, HMS Belfast, Tower Bridge, the Tower of London and much more:
https://www.thamesclippers.com/
From Tower Pier, follow the signs to Tower Hill underground station. Take a westbound Circle or District Line train to South Kensington and follow the signs to the museums.