Krakow has some of the best universities in Poland.
Well, in 2010 Krakow Jagiellonian University got better marks than Wroclaw University, but on the other hand Wroclaw University of Technology got better marks than both technical universities in Krakow... :
but all this rankings uni vs uni aren't very informative, because the better thing is to compare department vs deparment...
Krakow is a better city for inbound and outbound travel.
That is debatable also, it depends where you want to travel, for example there is much closer from Wroclaw to Berlin or Prague...
Wroclaw is less expensive overall.
That is true.
To sum things up, my opinion is:
- better public transport
- better university
- it is bigger city
- it is tourist destination (so friendlier for foreigners but more expensive)
- slightly better technical university
- it is smaller city
- it is much smaller tourist destination (well, there is no medieval castle here...)
- it has worse public transport and at least for another two years there will be problems with city jams
- it is a little but only a little cheaper here
Overall, both cities are fine students cities in positive way (there is easily above 100000 students in both cities every year), so I suggest you better focus on what kind of studies you want take and then try to compare departments
Good luck! :-)