You want to use remove menu page.
<?php
add_action( 'admin_menu', 'wpse26980_remove_tools', 99 );
function wpse26980_remove_tools()
{
remove_menu_page( 'tools.php' );
}
You can drop that in your functions.php file (without the opening <?php
most likely).
That’s not going to prevent people from typing in yoursite.com/wp-admin/tools.php
and seeing the tools page, however.