What's the best order?

I would suggest you do Prague and spend the most time there as well. That way you can wind down from all the long haul travel for short stay stops.

I'd look for a "multi-city" flight plan, flying into Prague and home from Warsaw.

Trains between Poland and neighboring countries are affordable but tend to take all day or all night; see How to Look Up Train Schedules and Routes Online. Flights may not be as frequent or cheap as between other major cities in Europe; see www.skyscanner.com.

Warsaw, Krakow and Prague don't have direct flights from the U.S. or Mexico. Anyway you go, you'll first have to go to one of the big European gateway cities to get to these cities.
You should fly into Krakow first, and then take a train up to Warsaw.
From Warsaw, you can take an inexpensive European budget air carrier down to Prague.
Then, fly out of Prague.
Our last train trips were from Budapest to Bratislava and from Vienna to Prague. They were slow, hot and not very pleasant. We prefer to fly budget air carriers whenever possible.

Hi,

I would take the train to get from city to city, took the train in 2001 from Warsaw to Krakow. I am sure the train is faster now than it was then. I would start in Warsaw.

Our last train trips were from Budapest to Bratislava and from Vienna
to Prague. They were slow, hot and not very pleasant. We prefer to fly
budget air carriers whenever possible

David knows I value his opinion, but the trip from Budapest to Vienna (about the same as the trip to Bratislava) is only hot in the summer (you are traveling in fall), and at 50 mph, not fast but adequate. I once booked Wizz Air from Varna to Budapest. The night before I get an email with a schedule change. The change? Departing a different city over an hour away ..... If we had a car.

Hi,

If you want to get a direct flight from the US to Warsaw, you need to get to Chicago first. The non-stop flight from Chicago is even less that from SFO to Paris or Frankfurt!

LOT Airlines flies direct to Warsaw from Chicago, JFK and Toronto, last time I checked.

I did these exact cities this past May, and started with Krakow, express train to Warsaw (about $15 US), short flight on LOT to Prague (about $180 US).

Warsaw had direct flights to Prague, whereas Krakow would have required a stop in Warsaw, LOT's hub. Prague was exhausting to me after 8 days in pleasantly busy Poland, so in hindsight I should have started in Prague, then to Warsaw and Krakow. All are beautiful cities and full of wonderful things to see, do and eat.

There are nonstops from NYC to Warsaw on LOT and seasonally to Prague on Delta. Not sure about September, but my guess is yes.

I would go Warsaw -- Krakow -- Prague. It makes the most sense geographically. Note that the train ride from Warsaw to Krakow isn't very long, but the shortest one from Krakow to Prague is roughly 8.5 hours, and I do not believe there are any nonstop flights between those two cities.

Actually, we took the train from Vienna to Prague in late August of this year and it was fine (clean, comfortable, fast, and air conditioned; plus a dining car available). They run very modern 'Railjets' now. I purchased the tickets (OeBB 'sparscheine') approximately 3 months before the trip and each ticket cost 34 Euros (1st Class) + 3 Euros to reserve the seat. The trip took 4 hours.

There is also seasonal direct connection between Atlanta and Prague by Delta.

I would try and start with the furthest one, Krakow, and work your way back. That seems like a lot of time for just those three stops. You could spend a whole week in Prague, I guess, with day trips. Prague is beautiful but light on must-see sights. We were there at the same time of year in 2011 and it was overrun with soccer tourists, not sure if that's the norm for that time of year. You might consider breaking things up and also stopping in Olomouc for a couple of night, which we visited on our trip. Very beautiful as well and without the crowds.