We like 'em both very much. It's pretty much a toss up - I'd give Narcoossee's the atmosphere edge and Citrico's the food quality edge.
Narcoossee's: more casual, louder (lots of wood so acoustics aren't great), lovely view. More families, if that matters to you. Almond cheesecake is my favorite dessert at Disney!
Citrico's: more "formal" (in the Disney way, not the real world way). Service is usually more attentive. Our kids were the only ones there - adrs at 6 p.m. - until the very end of the meal. In fact, the place was not half-filled so I think it is much easier to snag a last-minute adr here. Food, from appies to dessert, is consistently a small notch above Narcoossee's, I think.