You can use the Stage3D and Context3D classes to render graphics in an HTML-based AIR app. One issue, though, is that the rendering viewport is drawn below the Flash Display list. Well, the HTML display is part of that display list, so by default, your HTML display will obscure your rendering viewport.
There are a couple of solutions:
You can set the background of the HTML object to be transparent. This allows the rendered stuff to peek out from behind any text or other items on the page. See AIR docs.
The other thing you can do is to create a new NativeWindow to display the rendered content. Don't use HTMLLoader.createRootWindow(), since this will create a window that has an HTMLLoader in it. instead, use:
var renderwindow = new air.NativeWindow( new air.NativeWindowInitOptions() );
(Of course, you will want to set non-default window options in many cases.)