There are myths that one of Polish 17th century commanders during the so called "Deluge" - Stefan Czarniecki - carried out pogroms of Jews.
But I have researched some sources and I did not find any confirmation for these claims - on the other hand what I found out is that Czarniecki's troops pillaged settlements (villages and towns) of Greater Poland (which had the lowest percentage of Jews of all regions of Poland at that time) as a revenge for the betrayal of the province of Greater Poland to the Swedish king in 1655 (check wikipedia - the Treaty of Ujscie).
I found this from memoirs of Jakub Łoś (soldier who served under Czarniecki) in this article:
http://elear.salon24.pl/108465,jak-czarniecki-do-poznania-barbura-pogromil-powtorka
"Nasze wojska, nie więcej tylko Wielką Polskę zrabowały, tak pospolitego ruszenia jako i kwarciana hołota, za to że wpuścili Szwedów."
Translation:
"Our forces, both the levy en masse and the quarter rabble, plundered only Greater Poland, in revenge for the fact that they let in the Swedes."
And the same revenge described by one of ethnic Polish inhabitants of Greater Poland:
"O! Jakżeby opisać utrapienia od hołoty kwarcianych naszych. Niewypowiedziane ich zbrodnie, a spustoszenia wsiów i domów szlacheckich. To najcięższa, że im tak Szwedzi, jako wojsko nasze nie dokuczyło."
Translation:
"Oh! How to describe the worry inflicted by our quarter rabble. Unspeakable are their crimes and devastation of villages and of noble manors. But what is the most painful thing, is that even the Swedes were not as annoying as our own forces."
And one more account by an ethnic Polish inhabitant of Greater Poland, regarding crimes of Czarniecki's forces:
"(…

swawoli i rozpuście czeladzi wojskowej, która zabiegając czatami nie tylko wieśniakom, mieszczanom, szlachcie i dworom, ale nawet i kościołom nie folgowali."
Translation:
"(...) lawlessness and debauchery of military camp followers, who organized sudden raids not only against peasants, townsmen, nobility and manors, but even against churches."
When it comes to the term "quarter rabble" ("kwarciana hołota").
It surely refers to camp followers of the "quarter army" ("kwarciane wojsko").
So not regular soldiers, but camp followers and the levy en masse (general levy) were plundering.
And it should be noted, that the "quarter rabble" and the "levies", did it against the will of Czarniecki:
"Czarniecki wszystkimi siłami tego zabraniał, karał, bił, w ostatku zdybanych przy jakimkolwiek ekscesie natychmiast albo sam wieszać się kazał, albo i sam spod uwiązanych na drzewie, albo na wrociech konie zacinał (…

"
Translation:
This says what measures Czarniecki applied against "quarter rabble" and "levies" who were taking revenge on population of Greater Poland:
"Czarniecki was prohibiting this with all his strength, he was punishing, beating, as a last resort he was ordering those who were caught red-handed, in any kind of excess, either to immediately kill themselves, or he was hanging them personally."
This account says, that Czarniecki was trying to prevent those crimes very hard, he was punishing, beating, he was sentencing all those caught red-handed to death, sometimes he was even hanging them personally.
But Greater Poland had an opinion of a region which betrayed the rest of Poland in 1655 and allied themselves with Sweden.
===================================
So nothing specifically about Jews. Only that soldiers of Czarniecki considered inhabitants of Greater Poland as traitors (by the way, as I already wrote, % of Jews in population of Greater Poland was among the lowest in Poland). All of that was in revenge for the treaty of Ujście on 25 July 1655, when Greater Poland betrayed.
Apart from this I also found an article written by Eli Barbur (a Polish-Jewish journalist who emigrated from Poland in 1969 after he was bounced out of the university during events of March 1968) but he gives no evidences, just unsupported claims.