There are several international level organizations that issue and recognize rank. Obviously many national ones too.
The most famous is probably the original one the JKA or Japan Karate Association. This is the one founded by the students of Funakoshi Sensei, like the late Nakayama Matayoshi. The other ones can be credible too. I have friends who are involved in SKIF (Shotokan Karate-Do International Federation) which is headed by Kanazawa Sensei, a fromer student of Nakayama's.
Is there a World organization for Shotokan like in TKD. Or are they issued at the local level in each DOJO.