All of these organizations have strict standards for rank and for admitting new dojos. They do not get Aikikai ranks, except where noted.
The Iwama Shinshin Aiki Shurenkai under Saito Sensei's son (although they have no US dojos listed) is independent of the Aikikai Hombu.
Iwama in the US:
The Takemusu Aikido Association under Bill Witt Shihan
The Iwama section (Division One) of the CAA under Hendricks Sensei.
Neither was a fulltime student of O Sensei; both were students of Saito Shihan. They get dan ranks through the Aikikiai Hombu.
Japan Aikido Association/USA is associated with the Shodokan in Tokyo
There's an amazing array of quite respectable Tomiki style groups in the US, but they weren't founded by a first generation student of O Sensei and have no Japanese connection.
International Yoshinkan Aikido Federation, currently run by Shioda Shihan's son has several US dojos
Aikido Association of North America under Utada Sensei (who was a student of Shioda, but not so much a student of O Sensei). They issue their own dan ranks
Aikido Yoshinkan Yoseika, founded by Terada Shihan. In the US, it's under Parker Shihan.
I believe they get rank through the IYAF, or are registered through the IYAF.
founded by Noriaki Inoue, a nephew of O Sensei. They have several dojos in the US