It's very possible that the "high Rabbi" was the rebbe of Ger but it could have been the leader of many other Chassidik dynasties. Why do you believe it is him? From what I can find quickly online the center of the Ger dynasty was in Gora Kalawaria (Ger) which is closer to Warsaw than to Krakow. Ger was one of the largest sects before the war (and remains so today) and probably had a strong presence in Warsaw so he may have been a follower. 
I don't know off hand of a different Chassidik sect based in Krakow but as a larger city it would have had many shteibelach (smaller synagogues) connected to various sects. There could have been a big Rabbi who he followed there who wasn't a leader of a dynasty but had a large following. Also your mother may have remembered Krakow when in fact it was a smaller town in the area.
As far as why he would travel to visit the rebbe, he most likely went to spend the high holidays or another holiday there. It was and still is common for Chassidim to travel to gather with the sect leader for the holiday prayers. The rebbe would have spoken, and possibly give individual Chassidim blessings or counsel.