The Dreaming Jewels by Theodore Sturgeon
Horty Bluett is eight when he runs away from home. He'd been cruelly punished: Junky, the ugly old toy with the jewel-like eyes, the only thing that really belonged to him, had been deliberately smashed. And that hurt even more than having three fingers accidentally severed. Horty finds a new home among the freaks of a travelling carnival, protected by the beautiful midget, Zena. For Zena knows the truth about Junky and the jewels. She knows that Horty is one of the 'jewel people', and she knows what others would do to him if they found out that the jewels are living, thinking alien crystals from outer space.