I was in Kerala less than month ago. The only thing I regret was spending the night on a house boat in Alleppey. I wish I could go back in time, take a ferry or speed boat, spend the day in the lake and return to Alleppey city by evening.
I am not trying to cast any aspersions or discourage you from taking a house boat but here are few suggestions which might help:
1. Find a house boat which has open roof top for better views
In the evening at around 5PM they dock at some patch of land in the middle of the lake at their designated place; now you are 3KM away from the city and there is no going back until the morning, so
2. Don't go roaming outside after 7 pm or the mosquitoes bites will remain for 7 days, assured
3. On my house boat the A/Cs won't turn on until 7-8pm. They have dedicated power supply at the place they dock in the evening but it will take atleast couple more hours before the power is at it's fullest and A/Cs start cooling. In my case it was after 12AM
4. Buy your own drinks from the city because it's almost 3x times higher (150 for a beer) on the island
5. There is absolutely nothing you can do there
The only memorable moment was my younger brother leading me on the island and showing me things around (speed boats, crops, flowers, birds, fishes) as if he was familiar with the place. We walked almost 2KMs and did some bitching about how everything was so terrible there and returned to the house boat. Later in the evening I came to know that he had already walked in the opposite direction while I was sleeping that is how he was able to show me around.
Anyway, I wish you a memorable houseboat trip
