Golden Age Superman and the Earth-Two Superman might be genuinely alien as we have no evidence he ever had children with Lois nor any viable descendants.
Silver/Bronze Age aka Pre Crisis Superman is evidently human by the genetic definition of the species albeit by less rigourous species definitions he could still be considered alien. In numerous Pre Crisis stories, he's had descendants with Terran humans such as the Superman of 2465 and The Exile at the Edge of Eternity.
http://superman.nu/a/400/exile/Byrned Era Superman is evidently human going by Byrne's World of Krypton #6 where he specifically states this, the Armageddon 2001 stories where he interbreeds with Terran humans, Kingdom Come/The Kingdom & Jonathan, and the Superman Dynasty of DC One Million.
Birthright Superman seems to be possibly human going by the daughter Mxy says he and Lois could possibly have if they chose to have a baby. It remains unknown if this child would be viable or a mule, so Waid's incarnation is suspect for humanity at this point.
BTW, Tales of the Legion of Super-Heroes #325 confirms that Daxam and Krypton have the same genetic heritage and the two humanoid races are really the same one. Mon-El was taught that Daxam was the parent world and Krypton was the colony which jibes with the Kryp and Tonn story.