What is the difference between VP9 and ​WebM?
VP9 is a video format. Another example is H.264.

WebM is a container format that VP9 goes into. It is equivalent to the MP4 container format for the H.264 video format.

libvpx is a video encoder (or codec) which outputs the VP8 or VP9 video formats. Another encoder example is x264 which outputs the H.264 video format.