Can't comment on the London Dungeon, but I have to say, your itinerary looks horribly busy for 4 days, especially with a 9 year old.
If you've already booked and paid for London Eye, Shreks Adventure, Madame Tussauds and the Natural History Museum, then I would say that's plenty.
Tate Modern isn't very interesting for a child unless they are especially interested in art. Covent Garden and Borough Market are OK, but are really just shops/stalls.
London Eye and Shrek's Adventure are very close together, but for everything else, you need to factor in travel time - whether walking or using public transport, getting places takes time in London.
I'd suggest maybe a walk along the South Bank before/after London Eye/Shrek, there's lots of things to see, next to/on the river, but you can be pretty relaxed about it.