A lot of mods I've seen come with an "install.php" file, which they upload and execute to create/modify all the tables as required. phpbb itself even has one.
Just make a php script with all your SQL stuff in it, and say in your readme/install.txt that they need to upload and run it
P.S.: If you're modifying the existing phpbb tables, consider using the includes from phpbb - that way, you can do things like:
$sql = "ALTER TABLE " . USERS_TABLE . " ADD user_posts_frozen TINYINT(1) DEFAULT '0' NOT NULL AFTER user_posts";
...since it may not always be called "phpbb_users" (there's a configuration alias for every table phpbb uses!)