Okay, according to my Black/White game guide, N's last name is Harmonia. But according to this answer http://pokemondb.net/pokebase/97745/does-n-have-a-real-name which has Bulbapedia as a source, N's middle name is Harmonia. Is the game guide failing once again?
Game guides don't always get everything direct from the source, and are well known to have typos and other mistakes. I believe the latest game guide has an error in the type chart (saying Bug is super effective against Ghost or something like that).
The source for Bulbapedia is Game Freak's website itself. So his real name is Natural Harmonia Gropius and the game guide got it wrong.
One thing I've learned, Bulbapedia is always the way to go.
So yes, probably middle name.