We did the one night version- if you really want to relax 2 nights would be great, but the food selection (or lack thereof) might be a problem.
Side trips were very mellow, we did the tour of the floating village and then a short swim.
We booked thru the concierge, but i had looked at the website and it was about the same price. In the future I will do separate booking for a car, to get a better one. It's a long drive and you want a comfortable luxury car for this. The hotel gave us a fairly cheapo one and I wasnt happy with it. Make sure your driver understands where to take you, you'll likely arrive at this empty dock before the Bahaya comes in to pick you up. Grab a water and sit under the tree while you wait for the boat to pick you up.
I looked at the website for Bhaya, and the boat and cruise sound very nice.
Did you do the one night or two night cruise? Right now, I'm thinking the 2 night one is better because you'll have more time on the bay while the 1 night one sounds rushed. How were the side-trips (eg how much physical activity was required)?
Also, did you book directly with the company or through the hotel concierge? The prices on the website sound reasonable, but I'm wondering if booking via an agent will get an additional discount.