You can associate the label the following way:
OWLAxiom axiom = factory.getOWLAnnotationAssertionAxiom(newIndividual.asOWLNamedIndividual().getIRI(), label);
manager.applyChange(new AddAxiom(ontology, axiom));
In this case you need to work with a NamedIndividual
in order to retrieve the IRI to assert the annotation.