I'd say that bus to Magic Kingdom then monorail or boat to Polynesian is the best.
As you walk from the bus platforms to the monorail station you will pass by the big ferry dock and then the small launch dock. If you don't see the boat for the Polynesian at or arriving at the small launch dock, continue on to the resort monorail ramp.
As an aside, if you are adventuresome you could even take the (big) ferry if it is there, and at the other end of the line (Transportation and Ticket Center; MK parking) walk to the Polynesian.
You will generally miss the crowded areas at MK and environs on a Saturday night when transferring from bus to monorail etc. there. (Other than a momentary deluge simply crossing your path at a 90 degree angle for the MK turnstiles you are nowhere near when the big ferry unloads.) But if the bus queue at your resort (Pop Century) for MK is long (visible before you select a route and start) and you might not get on the first bus, you might try for the Epcot bus, then outside Epcot transfer to the monorail. At the end of the line (TTC) walk or take the resort monorail to the Poly'. Note that this is technically a three leg journey although as mentioned, one of the legs might be done on foot (no pun intended).
Are you actually going to Epcot. That changes the complexion of your itinerary and question completely!