I couldn't find much info about this so I thought I would post a little of what I have found since I have been here.
House boats Kollum.
Average price to Kollum to Alleppey was RS 14,000 - RS 22,000 depending on which company. Kollum to Kollum was RS 6750 - RS 10,000
DTPC. (one full day plus overnight). KOL to ALL RS 14,000 + tax
KOL to KOL 7500
Southern backwaters " " KOL to ALL RS 17,000 with AC
KOL to KOL 8000
Dream Cruise " " KOL to ALL RS 20,000 (nicest boat of the lot)
KOL to KOL 8500 (10000 with AC)
Saj holidays. " " KOL to ALL RS 16,000
KOL to KOL 6750
Visit kerala. " " KOL to KOL RS 7500
ALL to ALL. 7500 (nice boat)
When you walk down the road to the boat jetty you will be mobbed by all these guys and will have various flyers and business cards thrust upon you. It can be a bit overwhelming just with these few companies here in Kollum so imagine what it's like in alleppey with over a thousand! Insist on seeing the boat before you decide and try and meet the crew, remember you are going to be spending a long time with them!
Kollum to Kollum overnight.
You will get on the boat at 11.30 and chug up past the Chinese fishing nets to a point where you will moor up and have lunch. After lunch you will go a little further up the lake towards Monroe Island where you will stop again. From here you will get a guy with a small canoe to take you around the little canals this takes around 3 hours you'll see prawn farms, coir making and general life around the backwaters. Insist to stop some where with a good view of the sunset for dinner as if you don't you will probably get taken to the same place you had lunch! This is the last stop for the day. You should get an option to get some fresh sea food to supplement your dinner (all at extra cost of course) at a market or local village, If you want more booze this is the place to get it, if you stop the same place we did there is a government alcohol shop a short walk away.
Around 6 am give or take you can watch the sun rise before setting off back to the boat jetty where you will arrive at 9 ish.
If you wish to head to alleppey, ask when getting prices if they can include the ferry tickets to alleppey in the price (600).
Kollum to alleppey.
This runs the same route as the ferry. There is a large stretch of this run that is very dirty and unsightly. Personally I would not recommend this route. It is the same as above as far as stopping times and arrival but no canoe trip.
Alleppey house boats
From what I've heard and seen this is a very crowded route. There are literally hundreds of boats very where! You will moor up for lunch and dinner in great big lines of boats shoulder to shoulder.
The choice of boats however is much better than Kollum they range from floating crap barges to extravagant palaces with modern kitchens, rooms, decks and bathrooms.
To see the majority of the house boats go to the snake boat finishing point as they are all stored here. You should be able to walk along and see a good number of them and get a general idea of condition, size and shape.
We took a small boat in alleppey through the back waters through the smaller canals that the house boats can't get. It's less crowded and you feel a lot closer to the action. It should cost 300 rupees an hour. I would have been happy to just do this and not spend the money for the house boat because you don't miss much by doing it this way and it is a tenth of the cost.
Hope some of this was useful.