I'm almost sure he's dead but I think that Pein and the Rinnegan's secret have something to do with him, or even his dead body.
jiraiya is dead. he was stabbed in the neck a couple of times by pein, he lost copious amounts of blood, and was sinking into the water. what part of all that doesn't point to the fact that jiraiya is dead. in the interview kishi said that naruto is going to have to grow up just as shikamaru had to grow up. shikamaru grew up after the death of asuma so it's safe to say that jiraiya is dead. jiraiya's death is the driving force naruto needs in order for him to stop chasing after sasuke and start training.