I am from Alleppey and I know that lot of cheating s are happening related to house boats.I you want to hire a house boat, you can straightaway go to the boat landing station(alias finishing point) which is at a 15 MINS walking distance from Alleppey Bus Station.There , you can see a booking station for boats (Govt Operated, Yellow colored building) and book the boats directly from there.
They have got standard rates and packages and you will be having lot of choices of boats to choose from.The boats will be available from this place round the year and not need at all to prebook by giving double and triple the original charge, ,
Have a happy and safe Journey......