Actually, both are the same both use swig for templating, both of them use karma and mocha for tests, passport integration, nodemon, etc.
Both were started by the same people where Mean.js is a fork of Mean.io. Mean.io is now under the umbrella of the company.
Let's see what are the main differences:-
SCAFFOLDING AND BOILERPLATE GENERATION
Mean.io uses a custom CLI tool named 'mean' whereas Mean.js uses Yeoman Generators.
Mean.js uses modules just in the front-end (for angular), and connects them with Express. Whereas Mean.io uses a more self-contained node packages modularity with client and server files inside the modules.
Mean.io has recently moved to gulp but Mean.js uses grunt.