How to modify iFrame content in an admin thickbox

jQuery(document).ready(function($) {   
   $('.yourlink').click(function() { 

    tbframe_interval = setInterval(function() {
          $('#TB_iframeContent').contents().find('.savesend input[type="submit"]').val('changed the button text');
    }, 2000);
    tb_show('', 'media-upload.php?type=image&TB_iframe=true');
    return false;
   });
});

http://www.webmaster-source.com/2010/01/08/using-the-wordpress-uploader-in-your-plugin-or-theme/

you can also enqueue a script on the media upload page that should be available in you iframe, don’t know if that will do it though. am working on something very similar to what you are doing atm.

add_action( 'admin_print_scripts-media-upload-popup',  'kia_enqueue_script' );

function kia_enqueue_script(){
    wp_enqueue_script('prism-thumbnails','link to your script');
}