JSON is just a data format, it does nothing for you except describe data. SWF is Adobe's file format for vector graphic animations.
Do you have more info on Game Maker Studio supporting Spine animations?
SWF vs Spine, first there is obviously differences between the tools you use to make animations. Spine is designed to have a workflow for making skeleton animation for games. It has a slot system to make draw order and attachment switching sane, a skin system to allow reuse of animations with attachment switches when the skeleton looks different, etc. I'm not sure what runtime Game Maker will use, but the official Spine runtimes provide access to bones, attachments, etc at runtime which enables things like procedural animation (eg have your character point at the mouse location). I'm not sure how SWF will work in Game Maker, but I would expect it to be a more generic animation system. SWF is vector, Spine is raster (though not technically limited to raster, but rendering vector graphics is costly).
In the end probably both Spine and SWF will be able to animate some stuff, so it really comes down to what exactly you need. 🙂
