If you can possibly squeeze in the time to see both, they are worth the effort. When I was there in December 2000, I went to the GF one night by hopping off the monorail one night. Now, I've seen many Christmas trees, but my jaw literally dropped when I entered the GF atrium. I had never been into GF before, so the whole experience was impressive. What made it even more magical was that there was a choir performing in the atrium.
Later that week I took the behind the scenes Christmas tour, which included a stop at the WL. Although it was also a beautiful tree, it just looked like a bigger version of what you can find at any nice Christmas decorations store. The tour went there in the late morning, so the lobby was pretty empty. Maybe it would have been more effective at night.
If you are a fan of holiday decorations, I would definitely recommend the behind the scenes tour. It takes you to the World Showcase at Epcot, Main Street in the MK, the Osbourne Lights at the Studios (I know, no lights this year), and WL.