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