In this case, an enemy is a member of a defined group of characters you face throughout a game. For example, guards from original Wolfenstein 3D are such group. Guards are found in big numbers on all levels of the game and regarded as An enemy (because they all are the same spire, statistics and behavior).
Boss is an enemy created to challenge you and is used for a plot device as well.They are at most times the major antagonists in a series. They all are unique characters, usually have names and are much harder then regular enemies. The examples of bosses in Wolfenstein series: Adolf Hitler, Hans Grösse, Olaric, General Zetta, Heinrich I