Find which Safari window is playing video?
In Safari 9 (and probably later), a blue speaker icon appears in the URL bar of all windows whenever any window is playing audio. You can click on this to mute the current tab (if it's playing audio) or all other tabs (if the current one is playing audio). 

This icon also has a hidden feature: If you click and hold on it, you will see a list of all the tabs that are currently playing sound. Click on one of those, and the corresponding window will be brought to the front. Then you can stop that particular video.