I'll put in vote for Krakow too. It's a great place to see.
Prague I found a little theme-parkish. And in summer it's at its busiest so maybe save that for another time of year. But it is an absolutely beautiful city to see. Vienna.. nice, but meh.
And just to confuse you even more - I'll throw in one more suggestion: Budapest, my favourite in that part of the world (of the ones I've been to at least )
It depends on what you are looking for! I've never been to Krakow or Vienna but have been to other parts of Eastern and Western Europe, including Paris and Prague. If you are looking for the more historical side of Eastern Europe to get a good overall feel of the East-West dichotomy, I would say go for Poland. If you're looking for more quintessentially European cities, I would say Prague. I found Prague to have a lot of the same things going for it as Paris (food, fashion, must-see sites, entertainment) but with a lot more charm. Whichever route you choose, you will have a fantastic time!