I would choose Krakow. It’s a lovely friendly city with lots to see, full of history but slightly less full of tourists. Also close to Auschwitz which is well worth a visit and the salt mines which are absolutely beautiful.
I haven’t been to Prague but I adored Krakow - the Jewish Quarter has a lot going for it with loads of tiny pubs and bars and lovely shops. Wawel Castle is great too, lots to see and I found people really kind and helpful!