Agreed, It could be any of the "Admorim" (leaders of a Hassidic dynasty) .
Another option could be the Radomsker Rebbe, who would have been situated a bit closer to Krakow. At the time, it was a large movement and all of the Rebbes were either Shlomo Rabinowitz (died in the 1860's) or his direct male line descendants. Another event that would have spurred a pilgrimage would have been the funeral of the Rebbe himself (of course those weren't annual!).
One interesting fact: A number of Hassidic movements were consolidating throughout the 1800's and then continuously until after the Holocaust. That was one factor that made several of the movements very large.
Considering where your ancestor was from originally, I'd also guess it was the Gerrer Rebbe that he went to see. Perhaps it was easier to take a train into Krakow and then
ride by horse carriage (there might have been a few cars...very few) to Gur even though Warsaw was a bit closer? Either that or the Krakow thing is just a mistake or he followed a rabbi in Krakow that we haven't identified yet?
One thing you might want to do is use a reliable source to figure out if there were any INBERG marriages into the family of one of the big Rebbe's of that area. That could end up being an important clue.
Central Virginia, USA