I think that the Habsburgs and the Jagiellons had a fair amount of entanglement at some point, so it may be doable. Didn't the Habsburg inherit Bohemia that way?
However, I don't the think the Poles (and much less so, the Lithuanians) would be enamoured to the notion of being ruled from Vienna, especially as the relevant time is when the House of Habsburg was busy inheriting Burgundy and Spain as well.
EDIT: if such a union comes out stable and Bohemia is included (which is sorta useful to it staying together) I can see Prague being the capital.