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.
in the latest version of Safari, the Tab(s) which are playing audio/video will show a small Speaker icon on the right-side of the Tab. you can click on the speaker to Mute the audio. the address bar also shows the speaker icon with the playing tab is selected, playing in the foreground.