We have a big mono repo, however only one Meteor app. Basically we have tons of “plugins” that provide functionality, and these are all NPM packages (although currently we don’t publish them to NPM, API still too unstable). We have tried a bunch of approaches, currently we use yarn workspaces, which works great, and symlink them into the Meteor app to have Meteor do the babel etc (we did this externally before). You can check out our setup here: https://github.com/chili-epfl/FROG.
The only pain point is that Meteor doesn’t fully support yarn workspaces, because it refuses to look one directory up for a node_modules directory, so we do some automatic symlinking to get around this.