Travel

Unfortunately there is no direct flight. With a direct flight that would be the best option. The only direct train is overnight and that's probably the best option.

You can get some more options from http://www.rome2rio.com/s/Krakow/Prague

Depends how much comfort and convenience are worth to you. If you're in no hurry, and if going cheap is the priority, then bus or train are your better options.
Personally, I'd pay the extra premium to fly and thus arrive at my destination fresh, rested, and ready for an active day of exploring.

LOT Airlines flies Krakow to Warsaw and over to Prague in 3 hrs. approx. for around $205. It's not terribly expensive.

By rental car, it's about 6 hours--340 miles by the best roads.

By slow train, you're talking 6-8 hrs.. Buses are also pretty slow in Poland.

I discovered the lack of direct flights when planning my trip last May, so changed it to start in Krakow, train to Warsaw for a few days then direct flight to Prague. Of course if Warsaw isn't on your itinerary it's not helpful, but as another poster commented, LOT is a good choice even if you have to make a stop on the way to Prague--for the cost it's well worth the savings in time and energy.

http://www.studentagencybus.com/en/631_631/PRAGUE-KRAKOW
probably the easiest an cheapest.

I just received a tour brochure from a guide I have spoken to over the years, but never used. She put together a new tour from Budapest, Vienna and I think Prague through Slovakia to Krakow. The information looks very, very professionally done and through my conversations over the years I suspect she will do a good job.

Since getting to Krakow isn't the easiest mission and since Slovakia is such a stunningly beautiful country (a real Back Door experience) I though there are those here that might be interested.

Unfortunately she hasn't got a website. But if you send me a PM I can forward her contact information and maybe email the e-brochure she sent me.