That sounds like a nice choice to be caught between. As someone who's done a bit of travelling, I'd say that Krakow is pretty well located for places such as Vienna, the Tatras region in Slovakia, the Czech Republic, Hungary and so forth. Since you expressed an interest in Soviet studies though, I think Estonia's also not a bad choice since it's right next to the Russian Federation. It probably depends on how well connected your Estonian town is, though. If it's really hard to get in and out of, and travel is exorbitant (I've never been there so can't say) you might not be able to do so much travelling. Krakow on the other hand is exceptionally well connected. It really all depends - if you've already been to central Europe before then I'd say go with Estonia, if you've been to the Baltics before then go to Krakow, if you've been to neither, then, ummmmm, well... if I were you I'd probably go with Estonia, seeing that the modules are more to your taste, they're easier and you can practice your Russian. All those places in central Europe that you mentioned are REALLY easy to get to from the UK - it's a very well connected part of the world, and you could always go even if you didn't study there. I spent a month backpacking in that part of the world - flew to Budapest from London for 22 pounds, went to Vienna from there, then to Bratislava, then to Poprad, then over the Tatras to Zakopane and then Krakow - Auschwitz - Katowice. None of the intercity connections took over three hours, and none of the fares cost me over 10 euros. Accommodation is really cheap too - about 6-8 euros a night! Oh, but a quick PS - if you want to visit Auschwitz, don't go on on weekends, especially Sunday - none of the regular buses run then, and getting there and back from major hubs is a pain.
Ultimately, though, it's your call, and I reckon you'll have a great time wherever you end up going. Good luck