I've been searching for a way to get SQL scripts into OneNote while retaining syntax highlighting from SSMS for a long time now. It's seems unnecessarily hard: OneNote doesn't support RTF-formatted text from the clipboard, which shouldn't be a problem, since it *does* support HTML-formatted text. Unfortunately, its HTML rendering seems to lack support for the <whitespace> tag.
So pasted text doesn't generally work right.
Lots of folks use MS Word as a go-between, which makes the text look right, but Word uses the NBSP (non-breaking space) character for many of the spaces, which SSMS doesn't like at all.
Here's the best option available, I think, for OneNote 2013: http://notehighlight2013.codeplex.com/. I've used it, and it's just like the NoteHighlight 2010 plug in, with the advantage that the installer is in English. I love this, and I'm grateful to smsmith0 for porting this.
It also appears that Outlook handles things differently, so it mostly works using an Outlook email body as an intermediary for your pasted text from SSMS. NoteHighlight is better.