Not quite in Germany but Salzburg and Innsbruck have decent markets and enough around them to fill the time and both have cheap flights.
Munich was massive when I went but for some reason very badly served by cheap flights except from London.
One of the bonuses of the above three is that you have half a chance of being able to have a day in the mountains in the snow, which makes it more Christmassy!
easyjet seem to be pulling out of Cologne at the end of this season but if you're close to London you can get there for a similar price by Eurostar by booking through German Rails UK office (and getting the shopping back will be easier!).
One thing to watch is that in some places the market may only be on at weekends and some close down up to a week before Christmas (maybe the stall holders want to get their shopping done!).