As a data point, most Emigrants from Matera traditionally fly back to Naples and take the coach or train back. The journey may be longer than from Bari, but saving for the connecting time, additional flight time etc, I believe Naples works best.

the Flexibus Coach service, Naples to Matera cost approx €15 per person (single) and take 3hrs 45 minutes, with the added bonus of some countryside scenery (it will go up the Apennine Mountains past Avellino and Benevento and then down the spine of the same mountain).