There is the red flag boat; Wilderness Lodge to the Magic Kingdom.
The blue flag boat; WL to CR and Campgrounds, mainly for dining purposes. So, if you wanted to get to a dining ressie at Poly from WL, take the blue flag boat to CR and then take the resort monorail to Poly. It will stop at TTC right before Poly.
Yes, there is a boat from WL to MK . And you can take the boat to the CR from the WL, which makes it convenient when you want to go the GF and Poly too .