You can ABSOLUTELY do it cheaper. My husband and I went for a weekend to Crystal River in Jan 2000 especially to swim with the manatees. We stayed 2 nights at the Plantation Inn, which was wonderful, but you don't have to do that. The main issue for you, being in Orlando, is that the least crowded and best times to do this are just before the crack of dawn. We went on a Saturday morning, the coldest morning of the year, I believe. A sign on a bank said it was 30 degrees. You get to the dive shop at crystal river at 5:30am or so and after an orientation, they take you out on a pontoon boat and they search for the manatees. We had our own wetsuits and snorkel gear, so that may add to the price if you need to rent, but I think we paid around $50 each for the trip out. There was no one else out there when we got out to the manatees and it was magical, if frigid. By about 8 am, the river was swarming with people and our boat was all finished and we left. The manatees were also getting skittish at that point, so you don't want to spend your money to go late.
The manatees congregate in the springs when it is cold out, so I am not sure how many you would see if you go during warm weather. The spring is supposed to be a constant 70 something degrees, but after 2 hours, we were shivering uncontrollably and it took several hours (and a long nap back at the hotel) to feel warm again. I can't tell you how exhausted I was and I think it was from exposure to the cold. I would do it again in a minute, though. Amazing animals. I would definitely suggest spending the night before at the Plantation Inn so that you can get that early start, then go back to the room in plenty of time for a HOT shower, a great breakfast at the Inn, and a rest before the drive back to Orlando. I would not even consider doing it as a day trip and I don't know how long the drive would be - I am just talking the cold. The plantation Inn has a web site and I am sure someone there could help you find a company. I just can't remember the name of the dive shop we used - just be sure to find the one that goes out EARLY.
Good Luck!