The two restaurants that were amazing that I can remember off the top of my head were:
1. Latitudes: This is where I got engaged A boat takes you to Sunset Key Island and the restaurant was beautiful. It's beachfront dining and they had pretty great food. It's a bit expensive..I believe the entrees were around $25-30. I'm vegetarian and they were also very accommodating. The rest of my family isn't veg and they loved their food.
Latitudes
2. Conch Republic Seafood Company: They also had amazing food. Again, I'm vegetarian and they made me a fantastic dish! The rest of my family got seafood entrees and they loved their food.
Conch Republic Seafood
And oh yeah, I just remembered another one! There was this great Cuban food restaurant near Mallory Square.
El Meson de Pepe
Their food was also delicious!
I've only been to Key West once and it was for a few days so I'm no expert but I hope this helps out!