Crystal Doors No. 1: Island Realm by Kevin J. Anderson
Fourteen-year-old cousins Gwen and Vic have lived together ever since the mysterious deaths of Gwen's parents and disappearance of Vic's mother - until Vic's scientist father accidentally transports them through a magical crystal door to the island of Elantya. Cobblestone streets and silver towers mark the picturesque island, a trading hub and centre of knowledge that functions with a combination of advanced physics and sorcery.
Vic and Gwen are soon caught in a tempest of ancient magic: vicious creatures and fierce battles - all connected to a territorial feud with the sea-dwelling merlons, an age-old conflict between the bright and dark sages....and the cousins' own mysterious roots.