We've always enjoyed our meals at both. Kona will have a few "hot entrees", so there's a little more variety, plus appetizers and and different desserts besides ice cream. The Plaza sandwiches are great. Both have a wonderful salad (one beef and one is chicken).
Seems to me that the deciding factors would be (a) you like one menu better than the other, or (b) you want to take a break from the park and relax at the Poly for awhile -- or you really DON'T want to spend a lot of time for lunch and want to stay at the park.
I'd highly recommend both.