I'm currently reading Artemis Fowl (Paperback) by Eoin Colfer. I like the sound of "child prodigy" and "criminal mastermind", but I think the fairy part more or less ruined my good impression of the book. Take a look at the cover and blurb below:
Twelve-year-old Artemis is a millionaire, a genius and above all, a criminal mastermind. But Artemis doesn't know what he's taken on when he kidnaps a fairy, Captain Holly Short of the LEPrecon Unit. These aren't the fairies of bedtime stories -- they're dangerous! Full of unexpected twists and turns, Artemis Fowl is a riveting, magical adventure.