The boat ride from the Contemporary marina to FW and WL is a little shorter than the ride from MK. It's also a smaller boat, not much bigger than the Jungle River Cruise.
For maximum fun, I reccomend taking the boat from MK to FW, then taking the boat from FW back to Contemporary, so that you experience both. I love all of the boats at WDW, especially the open-water craft on Bay Lake, the Seven Seas Lagoon, and Crescent Lake.