Personally, I can't imagine a trip to Krakow without taking a day trip to the little town of Oswiecim, better know by the German name of Auschwitz. It's an easy, inexpensive train ride from Krakow and, once there, everything is within walking distance. You would first want to visit the converted Polish army barracks referred to as Auschwitz I with an excellent museum and historic information. From there, you can walk or take a very short taxi ride to the extermination camp known as Birkenau. This place is huge. So large in scale, that the Germans referred to the northern end of the camp as Canada and the southern end as Mexico. You could, potentially, spend many hours here. So, wear comfy shoes and pack a snack.
I've had the honor to make this pilgrimage twice in my life, first in the early '80's and then again in 2000, and it can be a very emotional experience. I hope you are able to add this destination to your journey. Please feel free to ask me any questions.
Safe and happy travels!