That should work. You'll probably get better results if you use a polarizer instead. Either way, you better have a fast lens or a high ISO. I don't think those movies are bright enough to photograph easily through sunglasses.
For those unaware of how the 3D movies work, they project two overlapping images. One image is polarized vertically and the other horizontally. The glasses you where are also polarizers (one vertical and on horizontal). Each glass blocks out the picture from on projector and lets in the picture from the other. That allows you to see a different image with each eye. Your brain puts them back together by infering depth where the images almost, but don't quite, match.