I would rather go to Krakow and make a day trip to Warsaw...
Seriously, Krakow is really a lot nicer than Warsaw in almost all aspects.

I have travelled between the two cities by plane and it takes only like 30 minutes, it's a pretty short flight.
The airport in Warsaw is close to the city centre, a taxi ride between Warsaw city centre and the airport takes less than 10 minutes.
The airport in Krakow is about 15 minutes by taxi from the city centre.
You could certainly make it in a day by plane as there are lots of daily flights but I would recommend you to stay at least a night in Krakow so you don't have to rush things.