3D nerd here. The answer to the original question is yes you can buy your own glasses for some of the shows, but it's not easy for all of them.
Most of the older 3D movies like Muppet-Vision 3D and Philharmagic use linear polarized glasses. The newer and more recently refurbished rides (notably Flights of Passage and Star Tours) use Dolby 3D (which is licensed from Infinitec-3D).
You can get a ton of different linear polarized glasses in different formats, including aviator style, wraparound sunglasses style, clip-ons, paper disposable, etc. Any linear polarized glasses will work, and mostly they're pretty inexpensive. Just search
Amazon for "linear polarized 3D glasses" and you'll find a ton of them. Just don't buy anything with colored lenses (those are primarily for comic books), or labeled for movie watching (those will be RealD, a different system), or that require batteries or are labeled "active" which are shutter glasses.
Most regular 3D theaters and home passive 3D TV's use RealD's system, which uses circular polarized glasses. Those will not work with any Disney show or ride. IMAX glasses should work, if you should happen to have a pair of them lying around.
Dolby 3D glasses are very complicated to produce and use multilayer filters. They cost, in bulk, something like $20/pair, compared with more like $1-2/pair for reusable linear glasses. They aren't sold retail by anyone (or at least I don't know of a source), because there's no real demand for individual pairs, and their system is very complicated to set up and use.