Actually chrome allows to do that, choose HTML files in Sources tab in Developer tools window. You will see HTML instead of javascript and simply add breakpoints in the <script> tags. Also you can add debugger; command to script what you want to debug. For example:
<script>
// some code
debugger; // This is your breakpoint
// other code you will able to debugg
</script>
Don’t forget to remove debugger;‘s when you want to release your website.