The number one attraction for kids is the Science Museum:
http://www.sciencemuseum.org.uk/
(NB: Once you get kids inside the Science Museum, you can't get them out! Allow at least three hours if you're only going for the free stuff or at least four hours if you're including things like the IMAX cinema presentations)
If you saw big queues at the Natural History Museum they were almost certainly for a special exhibition. You should be able to walk straight in to see the permanent displays:
http://www.nhm.ac.uk/index.html
(Some of the stuff would bore kids rigid but the moving dinosaurs are not to be missed!)
A trip on the river is fun but the guided tours are expensive (and too long for many kids). Instead take a regular river bus service for the short journey between, say, Tower Pier and Embankment (which takes in lots of sights). The crew usual provide a commentary anyway:
http://www.tfl.gov.uk/assets/downloads/river-tt-rb1-woolwich-arsenal-embankment.pdf
A trip on the Emiraate Air Line cable car across the Thames can be fun.
If the sun's shining, the street entertainers at Covent Garden Piazza provide some great free entertainment. Further summer fun is to be had at the Southbank Centre (by the Royal Festival Hall), where kids and adults alike can try to guess which 'rooms' of water will appear next:
http://www.southbankcentre.co.uk/find/hayward-gallery-and-visual-arts/other-art-on-site/past/jeppe-hein-appearing-rooms
(Although that link doesn't mention it, that feature HAS returned this year after missing last year through drought. Take some towels!).