I cannot say with certainty whether the museum is a “must see” as I was unable to secure tickets to the Schindler Factory in a visit earlier this month, However, based on the sites you will have visited by the end of your time in Krakow, I think it may not be vital that you rearrange your schedule solely to allow you to see the museum.
If you would like more history of the Jews in Krakow before, during, and after WW II, a comprehensive city tour with a good guide might be preferable. I was able to arrange a private tour for a group of eight with Rick Steves recommended guide Marta Chmielowska, and it was excellent. While Marta (and other good guides surely) will tailor an itinerary to suit your interests, our requested tour of sites she would recommend for someone visiting Krakow for the first time included a walk through the Kazimierz, the historic Jewish quarter of Krakow, including the Remah cemetery, a Jewish bookstore, synagogue, and sites that appear in Schindler‘s List; the ghetto, including the empty chairs exhibit in Ghetto Heroes Square, and the Eagle Pharmacy Museum, which someone mentioned previously (very small, well worth stopping in for as long as your time will allow). This portion of our full-day tour took less three hours, I think.