I've seen all three. As an adult I literally slept through half of the Lion King, but it is visually stunning for the kids. 11 year old might get bored.. It's also coming to the Grand Canal next year so I would be inclined to give it a miss on this trip.
Matilda is stunning. Tickets are pretty hard to come by but I would highly recommend it.
Shrek might be the best given the age differences in your kids though, something for both of them. It's also closing next year so it's probably your only chance. It's also available at TKTS most days so kinder to the pocket.
With any show I always say get the best tickets you can afford, which is why something like TKTS comes in handy to get top price tickets at the same price as seats in the Gods.