In the novel, the Raptors are indeed Deinonychus, but at the time Crichton wrote Jurassic Park Deinonychus was still classified inside the Velociraptor genre (it would get its own genre only later); thus, in the novel, we have two different Raptors: Velociraptor Mongoliensis (the baby the protagonists see in the Nursery) and Velociraptor Antirrhopus (all the bad ones), in reality Deinonychus. Spielberg found the name Velociraptor to be more menacing than Deinonychus and mantained the older classification - remaining loyal to the novel at the same time.
