The Science Museum's children interactive area is brilliant and free. Definitely that. You could also visit the National History Museum ob the same day, have a picnic in Hyde Park, go boating on the serpentine or have tea in the cafe at Kensington Palace and go to Diana's playground.
On another day, I think a boat from London Eye to Greenwich is a good idea. You see Westminster, Tower Bridge , Tower of London etc. Stop off at the Tower for a visit if you want, or just sail by. From Greenwich you can take the cable car, walk in the foot tunnel under the river, ride the driverless DLR trains. DC love being at the front. When mine were small, the conductor sometimes even let them push the 'Go' button, so they were the drivers. There's also Greenwich market for food, the park with playpark and pedalos, the Observatory if they're interested in weather and time, the Maritime museum which used to have a quite fun kids area where they could do Morse code to each other, parka virtual ship in a harbour, play battleships with a virtual cannon, and best of all, load and unload a ship using a toy crane.
A third day in the West End could be good - go to a matinee of a child-friendly show, have noodles in China town and those tiny fish shaped vanilla cakes for pudding. Visit Lego and M&M stores and Hamleys. Watch the street performers at Covent Garden.
If they are older, Shoreditch is good - the Street Art walking tour is amazing, the cool clothes, food markets and Brick Lane bagel and curry houses. Museum of London has some good stuff.