The London Transport Museum in Covent Garden is fantastic. Kids are free, you can get 241 tickets for the adults on this site, if you go by train: https://www.daysoutguide.co.uk/2for1-london
Mudlarks at The Museum of Dockland passes some time, and you can take the riverboat them from eg the London Eye (use Oyster - pretty sure it's cheaper with PAYG).
Also the Science Museum and Natural History Museum are fantastic for this age (and all ages!) Get the 345/49 to South Ken!