In File > Preferences > User Settings hide .js files when there is a matching .ts file.

{
 "files.exclude": {
 "**/.git": true,
 "**/.svn": true,
 "**/.hg": true,
 "**/.DS_Store": true,
 "**/*.js": {"when": "$(basename).ts"},
 "**/*.map": {"when": "$(basename).map"}
 }
}