Tangle, just been to the NHM with my 4-year-old and 6-year-old and they both loved it, although it's absolutely heaving at this time of year.
The Butterfly Explorers is really nice, they have some amazing ones in there and the kids get a little passport to stamp as they go round. It's a bit pricey for the 15 minutes or so you're in there, but you won't have to pay for your DD. If you decide to go, do the butterfly thing first and keep your ticket, as you can then skip to the front of the queue to get into the museum itself (otherwise it's miles long...).
Best things inside for little ones are the dinosaurs and the gallery with the blue whale - you have to queue for the dinosaurs too (no charge for them), although we were there before midday and didn't have long to wait - later on as we were leaving it was about 45mins to an hour .
You can take lunch with you and eat in the picnic zone, otherwise they have a nice (newish?) Deli Cafe in the Darwin Centre which was far more civilised than the main cafe in the entrance hall.
Other things the DC have enjoyed were Trafalgar Square (where you can feed those pigeons!), which tends to have lots of interesting stuff going on during the hols - last time I went there were 'giants' on stilts and strange creatures going round scaring the life out of all the kids .
The South Bank always has loads of things going on too, and is nice for a traffic-free stroll, down to the Tate Modern or Tower Bridge?
London Aquarium - were about to start a refurb last time we were there so check what's open.
Boat trip is fun from Westminster or Waterloo Pier down to the Tower of London or Greenwich (great for a picnic/ice cream and amazing views from the Observatory hill).
Other things I've fancied doing but not got round to yet (and cost a good deal more than any of the above) are the London Eye, the Duck Tour, or the open-top bus tour; will probably wait til they're a bit older for these.