I would definitely say Boma. On my trip before last, we stayed at AKL and had breakfast there every morning.The food is excellent. I also very much enjoy Ohana's breakfast, characters and all. And of course, Kona is always excellent too.
Definitely Kona - Love the juice, tonga toast and macadamia nut pancakes - and the Kona pressed pot coffee is the best.
My favorites are Boma and Fresh.
I also loved Spoodles, which has now been replaced by Kouzzina, but some of the menu items are the similar (for example, the vegetable flatbread). Anyway, Kouzzina's breakfast menu looks interesting and different than so many typical breakfast menus at WDW restaurants. My family will definately be trying this place on our next trip. You might want to check out the menu and consider giving it a try as well.