I never thought newbie or noob as derogatory either, in and of itself. it's moreso the way it's used. if someone says with a particular tone of voice that screams frustration "you're such a noob," no, that isn't going to feel good. that's a particular context, though.
I don't see fault in using Powder Monkey instead, but I do see that, as the term becomes more regularly used, it'll essentially be used the same way noob or newbie is now. someone screaming in frustration "you're such a powder monkey" isn't going to feel any less derogatory.