We have never done this tour, but we have rented a pontoon boat from The Port Hotel and Marina (
http://www.porthoteldivecenter.com/boat_eq_rentals.html) in Crystal River 4 times now and plan on doing so again December 26. For almost the price you're paying for one person you can rent the boat for 4 hours (very easy to maneuver if you've never driven a boat before). You have to watch a video about manatees and rules before they set you out since you are in the Manatee Wildlife Preserve. They give you a map and general instructions. If you don't have snorkel gear and wet suits (depending on the time of year and if you want one - we own our own snorkel gear that we bought at Target and have never bothered with wet suits) they rent those as well. We have gone in Feb, Jan, and Dec. Last time we went in early Dec and there were LOTS of manatees. Two in particular were very interested in us and one (who we named Gladys) stayed with us in the water for over an hour. We pet her and she actually played with us, it was though she was almost playing hide and seek!
Here are a couple of pictures of Gladys - if you have any other questions, don't hesitate to ask either here or you can PM me.