We (a bunch of academics from the UK) have just booked for a 3 bedroom Alleppey Roundtrip Houseboat with karmakerala.com for Feb 17, 2013. We chose their Premium Houseboat option - A/C after dinner till 7AM. They are headquartered in the UK (Scotland) and have a local team in Cochin.
Email exchanges and booking was exttremely efficient with prompt responses -- we paid 30% upfront through bank transfer.
Will report here on the experience since we did not find too many posts on karmakerala.