I agree that if using Disney Transport, there is only one best way to get from Pop to Poly, and that's bus from Pop to Magic Kingdom and then resort monorail from MK to Poly.
At Poly, the monorail station is in the second floor of the Great Ceremonial House. Both 'Ohana and Kona Cafe are also on the second floor of that building, making the monorail extra convenient for you.
Buses start running from the resorts to the parks around 6:30 a.m. or so, and the resort monorail starts running at 7:00 a.m., so you'll have ample opportunity to get to your breakfast ADR no matter how early it is.
If it's a VERY early reservation, like WAAAY before Magic Kingdom opens that day, it won't hurt to mention to the driver that you're having breakfast at the Polynesian, as there's a decent chance he/she will drive you directly to the Polynesian rather than to MK!