Looking at the code, you should be able to filter it. Something like the following should do it:
add_filter( 'emoji_url', 'wpse_232874_emoji_cdn_url' );
function wpse_232874_emoji_cdn_url( $url ) {
return 'http://example.com/my/cdn/url/';
}
…replacing http://example.com/my/cdn/url/
with whatever URL you want to use.