The ffmpeg manual states that:
libvpx-vp9 is the VP9 video encoder for WebM, an open, royalty-free media file format.
What is the difference between the 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.