Hi Shelley!
I love runDisney trips with my husband! I recently posted on the
runDisney blog about it.
This is a good question, and I have eaten at both places. My personal opinion is the Yachtsman Steakhouse. My husband and I ate there before the marathon this past January and the steak was the best I have ever had! (and that is saying something, as I love to eat)
The Flying Fish is a good restaurant, too. I am not a big fan of seafood, so I sometimes struggle at places like that to find exactly what I am looking for. If you love seafood, then you may like it best.
Be sure to check out Jellyrolls on the Boardwalk while you are there!
Have a great race, and let me know if you have any other questions:)