If you are using TypeScript nightly (and only with TypeScript 1.6 up) you can use in your tsconfig.json new property exclude which will mostly be used for node_modules like this
(more on this here : http://blogs.msdn.com/b/typescript/archive/2015/07/27/introducing-typescript-nightlies.aspx)
:
{ "compilerOptions": { "out": "../../built/local/tsc.js", "sourceMap": true }, "exclude": [ "node_modules" ] }
More on exclude property here : https://github.com/Microsoft/TypeScript/issues/3043