Eagles nest tour from Munich

You can get a train to Berchtesgaden, then it's a ten min walk to the documentation centre where the bus for the top of the mountain leaves from. If you're not in a mad rush then it's grand.
To be honest, any tour is a cod anyhow as you must take the special bus anyhow to the top so all you are doing is paying a premium to avoid a ten minute walk(which no doubt has a local bus connection anyhow)
Speed wise it is quicker by bus on paper, but the traffic jams on the motorway this time of year are fairly horrible so at least on the train you'll arrive at a predictable time.

The documentation centre is worth visiting too as it gives an overview of the crucial place that the area had in the nazi period. It's free in but not sure if there's a small charge on the audio guiðe.