Do you have Rick Steves Snapshot: Kraków, Warsaw & Gdansk? If not, get it right away. I found it excellent, and by reading about the attractions in each place, you can figure out how much time you will need in each. As a bonus, I see the new edition just came out, so it's as up to date as any print material can be.
I flew LOT from New York to Krakow (via Warsaw) and then back from Warsaw to New York. LOT was fine, and I'd definitely fly them again. One nice feature is that they offer Premium Economy for only about $225 more than regular economy. This not only has more legroom, but also wider and fancier seats (2-2-2 instead of 2-3-2 in regular coach). I stayed in coach, but the plane was still nice (a 787 as said above).
Two things to be aware of if you are flying through Warsaw to Krakow or anywhere else in Poland. First, these intra-Poland flights are on propeller planes (at least they were in 2013). I have no problem with these (the flights are very short), but I know some don't like them. And, if you're changing in Warsaw, IMMEDIATELY after passport control you go through security for your next flight. If I had known this, I'd have prepared better to take off my belt, have my 3-1-1 bag handy, etc (I had used things during the flight and wasn't expecting to have to deal with it so quickly on landing). Warsaw airport is otherwise very easy to deal with, as it's not a behemoth like Heathrow, JFK, etc.