If nobody comes up with a good explanation what makes the two tags different, we should merge stock-android (× 63) with vanilla-android (× 28), making the first (and more intuitive for new users) the master, and the second a synonym to it.
Note: Questions about this originate in the comments on Rename the 'firmware' tag to 'device-firmware' and make 'firmware' a synonym, where eldarerathis and I tried to untangle the mess with 'rom', 'stock-rom', 'device-firmware', and other tags, so one could catch some more background there.
And before somebody asks: yes, I know a stock-rom coming from e.g. Samsung is far from being vanilla. But what are people referring to when tagging a question 'stock-android' or 'vanilla-android'? The "least common denominator". Even questions explicitly tagged vanilla using the term "stock".