Narcoosee's is primarily a fish/seafood restaurant. It does have some chicken and beef options but if you want fresh fish/seafood then Narcoosee's would fit that bill. My DH said that Narcoosee's reminded him of a Rusty Pelican restaurant (not sure if they are nationwide, but think upscale seafood -- in the $25-$35/per plate range). Citrico's is a more land-based dining experience. The food is very different as it does not do much fish/seafood. I know the menus are posted either here or at allears.
Narcoosee's is right on the lagoon with a Magic Kindgom view. Not all tables can see the castle/magic kingdom but it's on the water. The inside is rather non-descript, I think, but you get a very open feel with all the windows. I know many people talk about booking a later dinner so they can watch the fireworks from there. Citrico's is in the main building and there really isn't much view other than the courtyard. The ambiance is much cosier, I think, and it has a bit more of an upscale feel in my opinion. Not stuffy though. It's open and bright and the tables are not right upon each other. I think they're too close at Narcoosee's. Just my thought though.
We ate at Citrico's last night and Narcoosee's the night before and we prefer Citricos. We are a party of 3 and DD5 liked Citricos menu better as well.
My suggestion would be to look at the menus for each and see if you would have a preference. If you're looking for fireworks/magic kindgom view for dinner then Narcoosee's would be the one but remember you may not get a window seat and may have to get up and go watch the fireworks rather than sit at your seat inside.
You didn't mention how many 'we' would be, but if you're looking for a romantic dinner then I'd definitely say Citrico's would be better. If it's just a good dining experience both will give you that. Nonetheless, check out the menus and see if you and/or your group would have a preference.
Hope this helps! Best Wishes!