African history is the stuff of multisemester college courses, so it cannot really be summed up in a single post. To try however: The correct answer is "All of the above". The vast majority of Africans during that period lived in tiny villages, just like their European counterparts. There were a number of kingdoms, centered around large cities, that ruled vast tracts of comparatively primitive people in the surrounding countryside. In between these large kingdoms were even larger areas where no "kingdoms" existed, but where control lay more in the hands of tribal confederations.
Aside from Egypt, the closest thing to an empire that arose was the Abyssinian (Ethiopian) empire, which controlled most of the African interior for many centuries. Control, of course, was a relative term back then. It generally meant that the people there didn't fight the Ethiopians, but there was little to no "rule" coming from the capitol. A decent map of pre-colonial Africa, though dated a little after the period you wanted, can be found here:
http://www.afriterra.org/MapImages/Mercator-1607/zoomify.html. You'll notice that Egypt and Libya are left out as seperate nations on that map, and are instead one big pink blob with Arabia. This was because of the Muslim conquests...Libya and Egypt were part of the Ottoman Empire by 1607.
The rest of the map is reasonably accurate in that it shows the approximate boundaries of the "nations" that existed at that time, and the locations of the major cities.