As stated, it all depends on the various operating hours, your location, your destination and even your park tickets.
The base would be a bus to Disney Springs and then a bus to your resort but different locations have different options. For your example, if the Magic Kingdom is open late enough you could take a bus there and then use the monorail, watercraft or even the walking path to get to the Polynesian Village. If you had been in Epcot that day and it is still open you could walk through the park to the monorail. If Disney’s Hollywood Studios is open late you could walk, take the Skyliner or boat to that park and bus to the Polynesian. Heck, if you wanted to be crazy you could even take every mode of transit at Walt Disney World: Boat from the Beach Club to the International Gateway, Skyliner to one of the hotels or even Disney’s Hollywood Studios, bus to Magic Kingdom and then monorail to the Polynesian.