I still say that calling Piper a Mary Sue is misunderstanding the intent of the books she's in. A Mary Sue is a guest character that steals the spotlight from the heroes.
A Mary Sue is an author-insert character who can out-logic Spock, out-engineer Scotty, etc. and has the whole crew gushing about how awesome she is. I think Piper qualifies. I mean, she defeats the Kobayashi Maru in the very first chapter.