From the Transportation post (post #14) of the very informative WL FAQ Thread
http://disboards.com/threads/disney...las-information-and-questions-thread.3372315/
RED FLAG: The boat to the left of the dock has a red flag and goes to the Magic Kingdom. The red flag boats operate from a half hour before the Magic Kingdom opens to an hour and a half after the Magic Kingdom closes. Normally, the MK/Red Flag boat is a yellow-covered boat. These boats can accommodate open strollers, wheel chairs and scooters.
BLUE FLAG: The boat to the right of the dock has a blue flag, and goes to Fort Wilderness and Disney's Contemporary Resort. These boats run from 6:45 AM to 11:30 PM. Passengers using wheel chairs/scooters can use the boat pictured above. Just let any boat captain know that you require a "covered" boat or handicap accessible boat.
Red Flag boat:
12 min to/from MK
Red/Green Flag boat:
20 min to/from MK via FW (Used at off peak times to serve both FW and WL with one larger boat.)
Blue Flag boat:
5 min direct to/from CR
5 min direct to/from FW
14 min CR via FW
14 min FW via CR