When we were there im October it took about 10 minutes. Boats have to go slow in the canal area by the Contemporary because of wake issues and other small craft in the water over there. Very enjoyable ride, though!
According to Tyler and the "Chip 'n Dale Express," the boat route will vary depending on the time of day. In the morning, it goes FW -> WL -> MK. After 3:00 P.M. it's WL -> FW -> MK. Boats run starting from 8:30 A.M. until 45 minutes after the Magic Kingdom closes.
Wilderness Lodge to MK takes about 10-minutes. Wilderness Lodge to Fort Wilderness to MK takes 20 -25 minutes.
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