If I copy it to my functions.php file it gets loaded AFTER the original declaration in post_functions.php.

Any way to do this?

Create a plugin, add the function to the plugin and make sure it loads first…

http://wordpress.org/support/topic/how-to-change-plugins-load-order

Here is better way.
Plz download attached zip, extract it and upload post_functions.php to godirectory > geodirectory-functions folder.

Then plz write this piece of code in ur theme functions.php

add_filter('geodir_custom_infowindow_html' , 'geodir_get_custom_infowindow_html', 10,3) ;
function geodir_get_custom_infowindow_html($html , $postinfo_obj, $post_preview = '')
{
	return 'Here u can copy content of geodir_get_infowindow_html function and can make necessary changes in html ';
}

Actually i have added a filter on that make that html alterable.

It will be included in next release too.

Thanks