I had to vote for a tie.
If you had asked me two years ago, I'd have said Dragon. If you had asked me six months ago, I'd have said Dungeon. Now...I just can't decide.
The fact is, thanks to Erik Mona and company, the magazines have both taken a very large turn for the better recently. Dragon is going to be doing an annual Campaign Classics issue starting next year, and it has gems like "Demonomicon of Iggwilv" that keep me coming back for more. Dungeon has its killer Adventure Path modules, and has works of art like Maure Castle, which are invaluable.
Simply put, I must have them both!