The mods will tend to see questions in threads on the main page, but the way to contact them directly is hn@ycombinator.com. (From the guidelines, https://news.ycombinator.com/newsguidelines.html)
I'm reasonably certain they are notified if the article is flagged, but I suppose it may not be the correct way of doing it.
AIUI flagging the article can also affect its ranking or kill it entirely, so it's probably not the best way.