I would recommend either the Kona Cafe at the Poly OR the GF Cafe. My favorite would have to be the GF Cafe, simply because I love the atmosphere and the food is really yummy! It's a very charming, out-of-the-way restaurant with great service.
Kona is a great place to eat as well, but it may be a little busier and noisier than the GF Cafe because it's located right next to the monorail exit/entrance for the Polynesian resort. However, if you're a coffee drinker, this is the place to go. I am not a fan of coffee, but my husband & sister in law said that Kona has the best coffee anywhere.
No matter which one you choose, you'll have a great time!