From what I understand, they both kind of refer to the same thing. Why the need for 2 terms?
Counterpoint is a type of polyphony with certain restrictions on form. For instance, contrapuntally organized music focuses on melodic interaction between multiple independent voices rather than harmonic interaction. In other words, chords occur as a result of coincident notes in multiple melodic lines rather than as a primary textural element. Other forms of polyphony have different restrictions (or, in the case of polyphony in general, no restrictions beyond having more than one voice).
I believe "counterpoint" is a narrower term (all counterpoint is polyphonic but not all polyphony is contrapuntal). Contrapuntal polyphony emerged in the late renaissance era and so medieval and early renaissance polyphony is not referred to as "counterpoint".