Repositioning ‘Reply’ Link in Comments

Use a custom callback to render the comment content. Inside of the callback function call comment_reply_link() wherever you need it:

comment_reply_link(
    array_merge(
        $args,
        array (
            'add_below' => 'comment-body',
            'depth'     => $reply_depth,
            // + 1 to offer always a reply link for a consistent UI
            'max_depth' => $args['max_depth'] + 1,
            'before'    => '<p class="reply-line">',
            'after'     => '</p>'
        )
    )
);