A surprising challenge to the historicity of the event is the lack of any clear reference in either the Qur'an or the Hadith to the event. The former only has an ambiguous statement in Surah Al-Hashr 59:15, usually applied to the Qaynuqah in relation to the expulsion of the Banu Nadir 'Like those who lately preceded them they have tasted the evil result of their conduct and (in the Hereafter there is) for them a grievous Penalty'
Yusuf Ali comments on the verse:
"The immediate reference was probably to the Jewish goldsmith tribe of the Qainuqa, who were also settled in a fortified township near Madinah. They were also punished and banished for their treachery, about a month after the battle of Badr, in which the Makkan Pagans had suffered a signal defeat, in Shawwal, A.H. 2. The Nadhir evidently did not take that lesson to heart..."
Yet there is nothing explicit in either this text or elsewhere in the Qur'an about the incident. Whilst there are several ahadith mentioning the Banu Qunaiqa, only one refers to their expulsion, and that is in the context of mentioning the general exile of the Jews from Medina.
There is no specific historical outline in the hadith corpus of the alleged event and why it occurred. Even Mawdudi said that, we have to rely on later Sira material, through which lens Muslim (and other) commentators interpret this verse. Even then, as we examine the supposed basis of the expulsion, there are grounds for suspicion that there were originally two distinct accounts involved – one involving Jewish recklessness, the other indicating a matter of honour, which Muslims like Mawdudi have redacted and merged, to reconcile their inconsistencies.
For one thing, we have no objective evidence as to the actual military strength or otherwise of the Qunayqa, and have to rely on later Muslim accounts. We cannot say for sure if the Qunayqa indeed provoked an incident one way or another, or whether indeed the actual event occurred at all. Moreover, even in the actual accounts as they stand, we do not encounter any supposed divine revelation arising demanding the exile of this section of the ahl-ul-Kitab because of their 'idolatrous' practices, as indicated in the hadith where Muhammad indicated his intention to exile the People of the Book for turning the graves of the prophets into places of worship.
http://debate.org.uk/topics/history/xstnc-7.html