I find most VCS software is not well suited to handling large immutable files (immutable in the sense there shouldn't be two different files with the same vendor, name, and exact version). With a distributed VCS, you probably don't want anyone doing a clone to have to download every version ever of every dependency.

A binary repository like Nexus or Artifactory is very useful for this.

To fix the npm instability problems, I use Nexus and configure it to proxy (and permanently cache) npmjs, and then use npm shrinkwrap.