A U.S. District Court judge in New York yesterday rejected government pleas that he delay action on 96 cases involving more than $3 billion in claims by American banks and corporations against Iranian government assets.

The Iranian funds are frozen under an order by President Carter last Nov. 24 in response to the seizure of American hostages at the U.S. Embassy in Tehran.

Earlier this month, Iran's Ayatollah Ruhollah Khomeini said the release of the Iranian funds was necessary before any of the 52 remaining hostages would be released.

If upheld, yesterday's order by District Court Judge Kevin Thomas Duffy would keep the Iranian funds in this country until all the claims are handled, case by case.

In the 40-page opinion, Duffy confirmed legal orders obtained by the banks and companies.

During the summer, both Treasury Secretary G. William Miller and Undersecretary of State Warren Christopher made in-camera representations to the judge in an effort to get action delayed until the hostages crisis was settled.

In deciding against the appeals of the Carter administration, Duffy said, "I must balance this request and the fact that the management of foreign affairs is the exclusive prerogative of the president with duties imposed on my office by the Constitution to fairly and justly decide issues brought before this court."

Louis Boudin, counsel for the Iranian central bank, said yesterday that he planned to appeal the ruling.

The claimants against Iran are seeking repayment for property seized by the Khomeini regime and contracts signed under the late shah's government that were abrogated after the revolution.

One other major group of claimants is banks that had loans outstanding to the Iranian government. When Carter froze Iran's assets, interest payments on these loans stopped and they were automatically thrown into default.

The largest of these claims is $366 million by the Chase Manhattan Bank.

Meanwhile, the U.S. Court of Appeals for the District of Columbia Circuit, which had received the same request from the government, agreed yesterday to a 90-day delay in the case of some American insurance companies that contend Iran owes them $35 million for the nationalization of their financial interests in that country.

In an unprecedented decision last July, a U.S. District Court Judge in Washington ruled in that case that Iran could be held liable for damages to American companies whose assets were taken over. That decision, which had been taken to the appeals court for review, was the first substantive ruling in any of the assets cases since the hostages were seized.