By default, singleton session beans are transactional (section 13.3.7 of the EJB 3.1 specification) and require acquisition of an exclusive lock for every business method invocation (sections 184.108.40.206 and 220.127.116.11). In contrast, a javax.inject.Singleton is not transactional and does not support container-managed concurrency (the major consequence being that no locking scheme is implemented by the container).
If you annotate your singleton session bean with @TransactionAttribute(NOT_SUPPORTED) and @Lock(READ), you should see significantly better performance, though there may still be some overhead. If you don't need EJB features, stick with @ApplicationScoped (javax.inject.Singleton is not defined by CDI, and its semantics are therefore not governed by that specification).
Thanks for the info. I had already annotated the singleton session bean with @Lock(READ) but not @TransactionAttribute(NOT_SUPPORTED). Since I don't need EJB features I will stick to @ApplicationScoped.