A rough scale of interest level for an 11yo when visiting the South Kensington Museums:
Science Museum: 10/10 (especially if you book for Wonderlab).
Natural History Museum: 7/10 - but it's important to be selective with regard to which galleries you visit. Some are really boring for kids but others are totally fascinating.
V&A: 3/10 - but there are still a few galleries that are worth a look with kids.
Note that the Science Museum and the Natural History Museum both require you to book (free) entry tickets online in advance of your visit. (Although general admission is free, some of the best exhibits require you to pay. Visitors to Wonderlab need to book both entry tickets to the Science Musem and to Wonderlab. Check the museums' website for information about other exhibits which require payment).
There's no need to book for the V&A though, so you can go to the Science Museum or the Natural History Museum first and then, if you feel like it, just wander across the road to the V&A).