I believe the black vs. shiny distinction relates to the age of the lens. A more important distinction is the number of elements in the lens design. As a general rule, the more elements the better. In many (most? all?) focal lengths, Nikon made at least two types of enlarger lenses: 4-element and 6-element. Unfortunately, the model names/numbers don't clearly indicate which design you've got. In the 50mm focal length, though, the f/4 model is a 4-element design whereas the f/2.8 model is a 6-element design. Thus, if you want a 50mm Nikon enlarging lens, the f/2.8 model is superior.
Of course, this assumes that the lens is in perfect condition. If an f/2.8 Nikon 50mm lens has been used as a hammer, all bets are off.