I struggled a bit today getting keyboard input working properly in Unity WebGL on Newgrounds, but finally have it working.
There's a couple of issues which might trip you up here.
Firstly, Unity's Input.inputString doesn't seem to work at all at the moment, so if you're using that you'll have to scan the keys using Input.GetKeyXXX.
Secondly, since NG hosts the game in an iframe, there's an issue with not having the focus set so that the game can receive key input.
You can fix this by changing index.html and adding the following to the <canvas> element:
onclick="window.focus()"
And also by adding this <script> block inside <body>:
<script>
window.onload = function() { window.focus(); }
</script>
Hope this helps!