Weather in Poland is a bit unpredictable in September and October - you can have a hot sunny day with temperature over 20 Celsius degree or cold autumn day with heavy rain. It's difficult to say :)
What is certain that the temperature difference in the seaside is not that significant. In Gdansk there's rarely a real summer or cold winter - it's always rather chilly and windy, so if you're not into high temperatures, then Gdansk might be just for you :)
I think it might be a good idea to organize your trip yourself and go for guided tours which will complement your stay. I've been using Get Your Guide and liked them - they have a lot of different options to choose from.
If you would like to get to know more about Gdansk and Krakow have a look at the below articles:
If you're in southern Poland, you might also want to visit Wroclaw - a beautiful city located on Oder river banks, also called The City of 100 Bridges (there are about 130 bridges in Wroclaw). What I like about this city is that there are lots of attractions but the prices are lower than in Warsaw, Gdansk or Krakow.