At the Contemporary Marina they have Sammy Duvall's watersports center, where you can do parasailing, water skiing, and personal watercraft tours. For more info check out: http://sammyduvall.com/
There is also the regular resort boat rental where you can rent pontoon boats, mid size Montauk boats, or the fun little Water Mouse boats. From there you can boat around the south end of Bay Lake and across the water bridge to the Seven Seas Lagoon where the Poly and Grand Floridian are.
Enjoy! Boating at WDW is a fun and relaxing contrast to a busy day in the parks.