The distinction between the two, as I understand it, is that a Master's prepared Clinical Nurse is on track to work as a Clinical Nurse Specialist in hospital, nursing home, or ambulatory settings. The Clinical Nurse Specialist role is one that encompasses five domains: research, teaching, leadership, clinical expertise, and advocacy. In many hospitals the CNS is the nurse specialist who is brought in to implement new best practices at the staff nurse level--so a lot of the job is translating research findings into practice via teaching new techniques or interventions to staff RNs.
The NP role, as I understand it, is much more linear in fashion. An NP is an expert clinician prepared at the master's level to delivery high quality care within the nursing model. So, you would be doing patient assessments, ordering tests/labs, diagnosing, prescribing and providing follow-up care. NPs work in many settings--outpatient, hospitals, nursing homes, ambulatory care, physician practices, and retail clinics in drugstores.
This is how I understand the two roles--hope this helps!