/faq says not to leave ““thanks!” or “me too!” [answers]”. It doesn't say anything about “thank you” comments being noise. The best reference I can find for that is a meta.SO discussion. That's neither official-looking nor discoverable (especially for users of sites other than SO).
Please mention that “thank you” comments should not be left on the comment privilege page. Proposed wording (to be added at the end of the “When should I comment?” section):
Please do not leave a comment just to say “thank you”. Upvote the answer instead.
It may be worth mentioning this on the main
In response to some comments: I don't want to forbid all comments containing “thanks”! While I don't care for them myself, I don't mind the occasional “thanks, this was exceptionally helpful”. What I do mind is new users who feel compelled to leave a “thank you” comment on every answer to their question; I want to be able to tell them to not do this and upvote instead, and I'm requesting some official page to refer them to.