I've been investigating this very thing, and what I found is the Web Browser control that it I think it is using (Microsoft.Dynamics.Framework.UI.WinForms.WebBrowserForNavigation) doesn't have a problem running as IE11. (It may not be officially supported but when has that ever stopped us...)
So, what you can do is redirect your page to one with the right headers and that will support webGL. e.g.
window.parent.location.href = 'https://get.webgl.org/';
Note: your code is sitting in an iframe, so you have to redirect the parent which also has the headers you don't want. This works for me.
Next step is to get the "corrected" header page generated with the rest of the Add-in files and get the extensibility interactions working back and forth to NAV. It's a bit ugly but I've managed to get the basics working...
--- EDIT 17/09/2015 ---
Oops, I've just realised this is a bad bad idea! This will break the NAV Web Client because it doesn't structure its iframes/divs in the same way as the Web Browser control on the Windows Client.
Instead I'm opening a child window using this code
childWindow = window.open(Microsoft.Dynamics.NAV.GetImageResource('ChildWindow.htm'), 'child', "width=500, height=500, location=no, menubar=no, scrollbars=no, status=no, toolbar=no");
For more info about this see my blog:
https://geeknikolai.wordpress.com/2015/09/17/how-to-include-non-image-resources-with-dynamics-nav-javascript-add-ins