Some times receiving iMessage notification on Mac is a annoying thing. Using same Apple ID for both phone and MacBook Pro make this problem. All messages from iPhone are syncing to MacBook iMessage app.
If you want to disable iMessage on OS X Yosemite, MacBook Pro, iMac, MacBook Air or Mac Mini, follow my steps.
Method 1:- (Permanently disable)
On the top left of the screen, click messages when it open. Then choose Preference under it.
In Message preferences, choose Accounts tab to remove accounts.
It will stop receiving messages from iPhone or iPad.
Method 2:- How to turn off iMessages on Mac
Unclick the “Enable this Account” box in Messages -> Preferences ->Accounts -> Enable this Account. And click Sign Out.
Just turn off iMessage notifications
Open System Preferences -.> Notifications.
Select Messages on the left and select None.
If you have any other doubts, do let us via comment.