My pair were 6 & 9 and they LOVED the Horrible Histories boat tour.
The open top bus tour was their least favourite.
They loved the tube and normal buses. If you use City Mapper App it's super helpful re what bus to get.
They loved all the different mini fountains that kids can play in. The one at coal drops yard was a favourite. They also have open air cinema in summer so they loved watching the lion king there too (which was free).
Also enjoyed going up the walkie talkie which is free, can book in advance.
They liked a walk along the Thames and Borough Market for tasty treats and atmos.
They loved Wahaca for their first Mexican, good kids offer.
They loved a musical Newsies that's not on any more but weren't fussed by Frozen.
Eldest is football daft so loved the Wembley Tour. Youngest loved dinosaurs and fossils so loved Natural History Museum.
Both loved going in the DLR give it's driver less and you can sit up front.
They loved the buzz of Covent Garden, street performers etc.
Daughter loved the V&A particularly the jewellery.
We did a Paddington walking tour that they enjoyed but was hard going for the 6 year old.