npm deprecate <pkg>[@<version>] <message>
This command will update the npm registry entry for a package, providing a deprecation warning to all who attempt to install it.
It works on version ranges as well as specific versions, so you can do something like this:
npm deprecate my-thing@"< 0.2.3" "critical bug fixed in v0.2.3"
Note that you must be the package owner to deprecate something.