Well...they are pretty different. The Tokyo Disneyland "It's a Small World" disc is cleaned up stereo. It's more like an accurate ride-thru than what has been previously released.
The Wonderland Music Store CD is an exact copy of the old 1964 New York World's Fair souvenir LP. It's mono and has narration telling you what you are supposed to be seeing. It's interesting historically, and it has some charm to it.
I recommend getting it just for historical purposes, and it really is a different listening experience than the Tokyo Disneyland CD.