There are many places where you can board a boat of on short or an other. During this trip we boarded a "regular" boat which took us from the Everglades close to the open sea.
During this narrated trip we saw lot's of birds and also some dolphins who followed this boat. You won't find this on a propellor boat which usually sails over shalow waters.
Picture taken december 2001
a canoe! a canoe trip is ESSENTIAL! You must go to the ranger's station and reserve a campsite first--it's a good idea because they'll give you a tide chart and rescue you if you get washed away. You should also go to a campsite because all the little islands and beaches fluctuate wildly with the tides; as Lonely Planet says, what may be above ground by day may be covered with muck by night!
You can camp on the keys and have a pretty little beach all to yourself or canoe down Turner River and camp on a chickee, which is a little wooden platform in the swamp with a portapotty attached. I personally found the beach incredibly wonderful, especially if you're sick of paddling all day. you can't really swim on the beach, as the water is muddy and full of sea sponges and other weird animals, but you get to see little coral reefs below (the water is relatively clear to 2 or 3 feet)--they're still cool even though they're not superflourescent.
we found it most convenient to rent a canoe from the shop beneath the ranger's station. It was about $25/day.