Either way you are going to have to potentially download a lot of stuff; I'd rather not have that bloat integrated into the repo. Also consider if you come onto a project and they've upgraded a library version multiple times, when you clone from the repo you are going to grab every revision they've ever used and checked in. This is going to be much bigger and slower than the equivalent npm install for that package.

If you are grabbing from an external repo, the spotty network is going to mess you up either way. If it's internal and your internet is that spotty, consider hosting a local npm cacheing server like this -- https://www.npmjs.com/package/sinopia.

My only issue with this technique is that 'npm start' and the rest aren't smart enough (please correct me if I'm wrong and there is a way to make it care!) to grab dependencies if you upgrade a dependency version and check that in.