I'm guessing you already have all the museums on your list, but I took both DSs (nearly 2 and 6.5) to the Science Museum and it was a big hit. It can be tricky to find stuff that they both enjoy but plentiful use of interactive exhibits plus sundry gadgets worked very well.
Princess Diana memorial playground in Hyde Park, my dc's love it there, huge sand area (too big to be a pit) large pirate ship, sound garden, little houses, water, grassy areas for picnic and an expensive cafe. Can only be admitted with children, it's at the Lancaster Gate side of the park.
Coram's Field, near King's Cross is very manageable with your ages and will give them all something to do - animals, sand, organised sport, climbing equipment, cafe, under 3's indoor/outdoor play area, paddling pool.
Don't plan too much... enjoy London at your childrens pace!! Check out this website for more ideas. There have been several threads recently... maybe have a look back at what has been recommended for other families.