Do it locally, cargo-companies are usually trustworthy. There are many cargo-companies in Germany, just look for the best price and ask what service they offer. You´ll find adresses of some of them (like Hellmann, GS-Sportreisen...) in Motorrad, Tourenfahrer or Motorrad-Abenteuer. In the past, I used GGG in Frankfurt, MBS in Cologne, the bike flew with Air Canada and Lufthansa to Vancouver and Buenos Aires.
For current information on shipping bikes check this site, there is a special section with shipping reports from all over the world.