How to block an email thread from notifications in Yosemite

You could use a Mail Rule to redirect them to a specific folder, that will stop the notification, if your prefs are set accordingly.
This is an example from my gateway notifications, which I don't need dinging & notifying every hour...

Stop evaluating as the last step if you want no further action, otherwise the next rules will be applied, down the list.

To stop them also making the new mail sound, I switch that off in prefs, then add this last Rule, right at the end, for any mail that wasn't redirected by a Rule on the way through...

To complete the setup, set these 2 prefs...