I had a look into RailEurope, and yes Bratislava is there. However, no direct line exists between Krakow and Bratislava, you'd have to transit twice. Total of about 6 hours 30 minutes, $75.
2:18PM/24 Apr Bratislava Hl S.
3:01PM/24 Apr Gaenserndorf 0hr 43min
3:05PM/24 Apr Gaenserndorf
3:52PM/24 Apr Breclav CS 0hr 47min
3:57PM/24 Apr Breclav CS 9:06PM/24 Apr Krakow Gl Osobowy