After Krakow I'll be in Warsaw for a few days (3rd week of May) and the more I read about it the more I think I need to visit Gdansk; the new fast trains take just under 3 hours, I could arrive around 9:30 am and head back to Warsaw around 5 or so. I travel alone so very good at moving swiftly and seeing a lot in a short time--some things just need a good once-over while others I might enter and explore a bit more, with time for a sit-down lunch. Is it worth it or am I just teasing myself?
I don't know, to spend 6 hours on the train just for few hours in the city like Gdansk? Personally I would do it at least overnight. Right now I am in process doing my homework about Warsaw and Gdansk because that's where I will be at the end of May and beginning of June.
I think it would be worth it. You have enough time to do a fair amount of strolling and if you discover you really like it, you'll probably be back (Marlbork Castle would be worth linking to Gdansk but requires more time than just a day trip like yours). Gdansk is definitely a great city to visit and you probably won't regret it.
I have been to Krakow, Warsaw and Gdansk. All 3 are very different, and I think it will be well worth your time to visit all 3.
If you decide to go to Gdansk, I would recommend spending a few hours around the old town area. St. Mary's church is beautiful, and definitely worth climbing to the top to get a great view of the entire city. I also feel it's worth a visit just for the historical significance with the shipyards, Lech Walesa's office, etc. Of course, the crane is one of the big attractions as well. Gdansk is also very famous for it's amber, so you will find a lot of shops that sell jewelry and other things with amber.
If you have the time, I would also suggest taking a bus to Sopot, which is just outside of Gdansk. It's a beautiful resort town on the Baltic Sea. There is a huge pier that you can walk out on, and look back to the shoreline and get really nice views of the beautiful hotels on the beach.
My husband and I will be going back to Gdansk and Warsaw this fall, and can't wait to get back. I hope you enjoy it!