I liked staying at the Aparthotel Ma?y Kraków (http://pl.maly-krakow.pl/home). Check it out on Trip Advisor (http://www.tripadvisor.com/Hotel_Review-g274772-d626463-Reviews-Aparthotel_Maly_Krakow-Krakow_Lesser_Poland_Province_Southern_Poland.html) as well.
Close to the Central Station and Center, good size room with kitchenette etc. It's behind the buildings on the street so a bit hard to find the first time, but I would stay there again. No view, however as I think it was all one floor, or that's all I remember.
They had actually booked out my room to a larger group that wanted a few more rooms and in return for the one night, they set me up for free at the Hotel Wyspia?ski which was great. Larger room over looking the Center (behind trees), but I had a balcony and everything. Wanted to actually stay there and pay the difference, but I didn't. Either one of those are both good hotels, but the Aparthotel Ma?y Kraków will be cheaper.
That's my suggestion anyways...