First visit to these cities and need advice on the best way to travel between them .....bus, flixbus, or train. Also where to I need to go to book tickets and look at timeframe. Sorry, just need some guidance!

Train, without a doubt.

https://www.intercity.pl/en/

Express Intercity Premium trains (EIP) are the fastest and most expensive.

InterCity (IP) are considerably less expensive and almost as fast as the EIP trains.

Twoje Linie Kolejowe (TLK) taken longer due to more frequent stops, they also use older rolling stock.

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If you go by train -- and that wuold be my choice, too -- consult seat61.com for info about how to book, etc.

I don't know what's best, but we took the train and it was simple and inexpensive.

If you decide to take the bus, consider the traffic direction and congestion. On Friday afternoons, the road will be busy, both in the vicinity of Krakow and Warsaw. The same applies before national holidays. You did not specify the dates and times, so I warn you that you may get stuck in traffic jams if you travel at an inconvenient time. I also usually check Google Maps for roadworks, as they can paralyse the ring roads of large cities. The train is the best option in such cases.

Express Intercity fast train is what we took last year, most convenient option IMO.

I just took the train, i don't know why you'd take a bus. The fastest trains, EIP or EIC, take less than 3 hrs. I always buy train tickets from a country's rail company site. For those, I think it is intercity.pl

Thanks to all! Train it is!