You have a few options available to you, it's been a little while since I've tried them out so I would recommend seeing which works for you.
1. Adding a reference comment to your JavaScript file
The JavaScript editor built into Visual Studio allows you to extend the JS intellisense by adding references to JavaScript files via the following comment that should be placed at the top of your JavaScript file.
/// <reference path="../app/your-transpiled-ts-file.js" />
2. Referencing JS files via Visual Studio's options
You can also do a similar thing on a global level via Options > JavaScript > IntelliSense > References.
See this article by Mads Kristensen for more information.
3. TypeScript's allowJs option
One of the new exciting features in TypeScript (1.8 I believe) is the allowJs flag that can be set to true within your project's tsconfig.json file.
Enabling this allows you to use TypeScript definition files within JavaScript and get the full intelliSense experience you'd expect.
Here's a video of TypeScript's creator, Anders Hejlsberg demonstrating this at the recent Build 2016 event that I'd recommend taking a look at (I've linked directly to the part where he starts to talk about the allowJs flag).