I typically add this it at the top of my main application typescript file… here’s what my boilerplate looks like (my app.ts sits in a directory on the same level as com/ where I keep other scripts).
///<reference path='../com/jquery.d.ts' />
///<reference path='../com/webvr.d.ts' />
///<reference path='../com/three.d.ts' />
I can’t help with Ionic or Heroku specific issues since I haven’t used those frameworks. I write Typescript in Eclipse and I’ve found the IDE is a bit finnicky sometimes in picking up the definition files, but you should only need to reference them once per project (not once per document). Failing all else, you should be able to paste the webvr.d.ts interfaces into the three.d.ts file outside the THREE module.
Additionally, check that you are using the latest three.d.ts file. It doesn’t look like it.