Both destinations are served by Lohegaon (PNQ). Since there's no flight route between them, the best way to travel is by road.
Pune
Fly to Lohegaon (PNQ), then travel by road to Pune. Taxis, buses, and private cabs are available from the airport.
Baramati
Fly to Pune (PNQ), then travel by road to Baramati. Local transport options include taxis, auto-rickshaws, and state buses.