Benjamin H. Kean, the doctor who said the deposed shah of Iran was so ill that treatment in the United States was desirable, has sued a scientific magazine for saying he made a "superficial" and misleading diagnosis.

Kean's diagnosis led President Carter to order the shah's admission to New York Hospital-Cornell Medical Center in October 1979, which triggered seizure of the U.S. Embassy in Tehran and the hostage crisis.

An article in a January issue of Science, the weekly magazine of the 130,000-member American Association for the Advancement of Science (AAAS), said Kean went to Mexico to examine the shah as "friend" and, in effect, agent of banker David Rockefeller, who argued that the shah should be given refuge in the United States.

Kean told the State Deparment the shah was gravely ill with lymphoma, or lymph gland cancer, and a blocked bile duct. The lymphoma ultimately killed him. But the immediate problem that fall, Science said, was a gall bladder disorder that could have been treated in Mexico.

In a suit filed in U.S. District Court here, Kean said his diagnosis was careful and accurate. He called the Science article libelous and "scurrilous" and is seeking $4 million in damages, claiming that the income from his New York practice has been reduced from $100,000 to $50,000 annually.

Kean said yesterday he had never met Rockefeller before the shah's treatment in New York, and he declined to say who asked him to visit the ailing monarch.