However, when I try to create a new project for the Pycom LoPy, it doesn't show up in the boards list. It looks like something is wrong with the plugin?

Here's screen shot showing the plugin is installed.

Here's another when I'm trying to add a new board, pycom/lopy doesn't show up. Where is it in your system? Am I just blind?

It looks like you are using PlatformIO, this is not something we currently support. Pymakr is a standalone plugin for atom and does not interact with platformIO in any way. To create a pymakr project, just create a empty folder on your computer and open it with atom. You can then add project settings via the settings menu in the Pymakr panel and create a main.py file.