There were Jews in Medina who were there for hundreds of years before Muhammad (Yimach Shmo Vezichro). He expelled and killed them after they wouldn't recognize him as a prophet.
I don't believe there were Jews in mecca.
I heard about Jews in Mecca who were assasinated and also some sold as slaves. I have even heard that Muhammad made a parody of Jewish law about Hallachot regarding war with hostile cities outside Eretz Israel. Islamic sources use to say "Jews of Mecca" when explaining hate verses, so as to imply that anti-Semite verses only refer to that particualr "war" and hide the fact that they hate all Jews.
Now, if you have source about a massacre in Medina, it would help very much. Especially if not written by Arabs. The reason is that all hate and massacres in the Hadith is already widely known. Arabs approve it, and non-Muslims either do not believe in it or prefer to act if they don't. It would also be helpfull to find documents about the destruction of other minorities.
Let's see... we have commemorations of nearly all genocides known in history. If this is accepted as a historical fact, we should also recognise the non-Muslim genocide in Arabia.
The great difference is that all other massacres were either not commited in the name of religion, or if done on behalf of religion, they were not historically endorsed by any prophet or prohet pretender. If Muhammad is historically recognised as guilty of genocide, it would render Islam officially equal to Nazism.