Stephen E. Smith, a financial analyst and political strategist in the Presidential campaign of his brother-in-law, John F. Kennedy, in 1960, died in 1990 at his Manhattan home. He was 62 years old. Mr. Smith not only managed many of the Kennedy family's political campaigns, but ran several Kennedy businesses and served as an adviser in family financial matters. In 1956, he married Jean, the youngest of the Kennedy daughters. Mr. Smith was born at Bayport, L.I., on Sept. 24, 1927, and grew up in the Bay Ridge section of Brooklyn. He majored in history at Georgetown University, where he received his bachelor's degree in 1948. He served with the United States Air Force in 1951 and 1952 and became a first lieutenant. He joined his family's business, Cleary Brothers Inc., which operated tugs and barges on New York's upstate canals and in New York Harbor. He then headed the Park Agency Inc., in Manhattan, where he managed $300 million in Kennedy family investments. Mr. Smith is survived by his wife and four children, William, Stephen Jr., Amanda and Kym, all of whom live in Manhattan and were with him at his death.