The short answer: do Alleppey if it’s your first time, Kumarakom if you’ve done backwaters before. The longer answer is more nuanced.
Alleppey has the larger, more developed network of canals — you’ll cruise through villages, see traditional fishing, eat lunch at a 100-year-old toddy shop, and see the famous palm-lined narrow canals from the brochures. It’s busier (50+ boats can be on the same stretch in peak season) but the variety is unmatched.
Kumarakom is quieter. The Vembanad Lake stretches wide and open, you’ll see far more birdlife (especially November-February), and the houseboats tend to be larger and more luxurious. But you spend more time on open water, less on intimate canals.
Our recommendation for first-timers: 1 night Alleppey houseboat. For repeat visitors or premium honeymoons: 1 night each, with a private transfer between.