Here's a breakdown to decide which one is best for you.
Character
Munnar is located in the Western Ghats mountain range, known for its stunning scenery of rolling hills amid lush tea plantations.
Alleppey on the planes with expanse of coconut palm fringed serene backwaters, network of canals, lakes, and rivers.
Activities
Munnar is action packed with hiking, trekking, mountain biking, boating, sightseeing, plantation visits are so on.
Alleppey is all about laid back toursin with Houseboat cruises, canoeing, fishing, birdwatching, and when you're tired of it, visiting beaches!
Climate
Munnar scores hand down! Munnar has pleasant weather year-round, with cool nights, of reasons for its popularity.
Alleppey is hot and humid, typical of a coastal town. Not many enjies this weather for long as a tourist.
Schedule
You can experience Alleppey in a day and night. If you are tight on itinerary , go for Alleppey, you'll not regret.
Munnar needs at least 3 days to get a fulfilled feeling. A whirlwind tour is not possible with Munnar.
Attractions
Everything in Munnar is spread out in a mountainous terrain. Munnar has a lot options.
Alleppey don't have many options ( backwater & beach), but that's the highlight.
Food
Alleppey scores by a wide margin, esp if you are seafood lover. Dishes from the fresh catches is the order of the day.
Munnar's cuisine depend on the type of resort you've checked in.
Access
Alleppey scores very high. You can arrive Alleppey by train. The highway passes by Alleppey and it's more urban. In 2 hours you'll reach Alleppey from Kochi airport.
Reaching Munnar is a 5 hours excruciating ride to cover 120km.
Lifestyle
Alleppey has better options to experience Kerala's unique culture.
Munnar is more of a plantation town.
Conclusion
For a refreshing escape in the mountains with plenty of outdoor activities, Munnar is the better choice.
For a laidback cruise style experience on the backwaters and a chance to experience Kerala's unique culture, Alleppey is the better option.
Who goes to Munnar ? Nature lovers, adventure junkees, bikers, couples, families.
Who goes to Alleppey ? Those looking for a relaxed vacation, foodies, couples, families.