Our recent hotel finds, in Krakow, include:
Hotel Unicus: This is a small, boutique hotel with 35 rooms, right off the Florianska. The rooms are contemporary and well-appointed. I loved my double-deluxe room with a king bed. The only drawback was that it was facing Florianska where you did hear some pedestrian noise. Just bring earplugs. They had a lovely dining room downstairs for breakfast with old brick arches and walls. The staff was very helpful. It is a perfect location from which to explore the city. Swietego Marka 20.
Copernicus: For a more formal option, this is a good choice and a lovely Relais & Chateaux property. Kanonicza 16.
The Bonerowski Palace is another traditional option in the heart of Krakow at Rynek Glowny 42.