They are both excellent restaurants and both are among my favorites in WDW. I guess it comes down to what you are in the mood for that will determine which restaurant you should go to. Flying Fish, does offer beef dishes, but the seafood is what stands out here; and they do a very good job at it as well. Yachtsman Steakhouse does offer seafood dishes, but the steaks are what they are known for and are excellent. I would rate the service as excellent at both and give the edge to Flying Fish for decor. Either way you won't go wrong and will leave happy and full.
If you are paying OOP instead of the
DDP, I would recommend Blue Zoo for seafood and Shula's for steaks. They are both nearby at the Swan/Dolphin and IMO, they are both better than Yachtsman and Flying Fish. When I'm not on the DDP, both of these restaurants are always on my list.