Is it possible to edit some code in Notification Center to allow Facebook messenger notifications to have a "Reply" or "Close" similar to iMessage?
Is it possible to code a “reply” to Facebook Messages in Notification Centre in Maverick OS X?
No. As of 10.9.1, Apple has not added the ability to do so, and unfortunately, you're going to need to wait on Apple to do this natively.
I can, however, suggest an app that you can try. It's called Chat Heads and it works really well. It's available in the Mac App Store for free.
Here's the link: https://itunes.apple.com/ca/app/chat-heads/id670724330?mt=12