Prussia was formed after Bohemia became part of the Habsburg domains.....so itd be a Habsburg
There could easily have been a Bohemian Brandenburg. Indeed there was one until 1417 when it was leased to Frederick of Hohenzollern by the then Bohemian King.
Take away that decision and Brandenburg at least remains an appanage of the Bohemian Crown. Whether it ever acquires East Prussia etc is another matter.