Hm... Strange... very strange... I always thought both of them were females... And Manaphy has proof of that, I mean look at the episode/movie it appears in, its voice is very feminine. But, hey, we all have out preferences.
It is a pokemon!, ashs voice is made by a woman does it mean he is a woman? No. Manaphy is called the prince of the sea, i have watched the movie 4 times and im a huge fan of pokemon XD Both are genderless though.