Crystal River is almost always very crowded. Although it is a popular place to see manatees, the main reason for this is because the cities economy has been built on manatee tourism, so they advertise, a lot. As a result, you will usually see a ton of people here. There are at least a half dozen better places to see manatees in Florida that also have crystal clear water. Some of the best places to see manatees are in places that they gather during the summer. These places don't usually have crystal clear water, but the manatees are much more active than when you see them gathered in the cold months at places like Crystal River where they are often just huddled together not doing much of anything but trying to stay warm and survive the cold days.
There are also other crystal clear rivers and springs near Crystal River where you can see manatees all year long without the big crowds of people such as the Chassahowitzka, Homossassa River or the Fort Island Trail. Trey Walker (910) 789-2181 does Manatee tours in See Through Canoes in this area and can take you to where the manatees are any time of year.
St Petersburg, FL is one of the best places to see manatees all year long.
Best places to see manatee in Florida
Kings Bay is at the end of Crystal River and there are at least 29 springs in the Kings Bay area. The water from these springs is usually 72 degrees. The most popular of these springs is Three Sisters Springs. There are a few different parks and other places where you can launch your own canoe or kayak if you already have one.