Cardinal Terence Cooke came late to the highly charged St. Patrick's Day parade here today, managing to honor the Irish while publicly snubbing Grand Marshal Michael Flannery, a vocal supporter of the Irish Republican Army.

The tall brass doors of St. Patrick's Cathedral were shut, the steps were empty and the traditional red carpet was missing when Flannery, 81, wearing the regulation tall silk hat, tie and tails, passed by on Fifth Avenue at the head of an estimated 100,000 marchers.

Half an hour later, the cardinal appeared on the steps of the cathedral to scattered boos from the crowd.

Cooke seemed unperturbed. "I'm surprised it was so few. I expected a lot more," he said.

Cooke spoke privately with Flannery for 10 minutes before the start of the parade, condemning ongoing sectarian violence in Northern Ireland by both the IRA and Protestant groups and telling Flannery that, "because of the attempted misuse of the parade to support such continuing violence," he would not review the event, according to a diocesan statement.

"I said we have a political process and that is the way to peace" in Northern Ireland, Cooke told reporters later, "and as an Irish gentleman he said, 'I understand.' "

The cardinal joined the Defense Department, the government of the Republic of Ireland and several prominent politicians, including Sens. Daniel Patrick Moynihan (D-N.Y.) and Edward M. Kennedy (D-Mass.) in boycotting Flannery, who was named grand marshal in an open effort by Irish-American groups here to turn the parade into a political statement.

"The theme of the march is justice and peace," said Flannery before the event. "Let's pray to almighty God to give our enemy Britain the wisdom to get out of there Northern Ireland ."

Cooke's decision to ignore Flannery was a clear thumbs down from the church on Irish-American support, both rhetorical and financial, for attempts by the provisional wing of the IRA to bomb the British out of Northern Ireland and unite its six provinces with the Roman Catholic Republic to the south.

Asked if he had consulted with the Vatican on his decision, Cooke said, "Not directly. They know I can take care of things here."

Flannery, whose stooped, white-haired figure towered over the other parade officials, was applauded as he took his seat at the front of the hushed cathedral for the pre-parade Mass. Beside him in the front-row pew was Robert McCann, director of the Irish Northern Aid Committee (NORAID), a charity group that the Irish government has accused of providing arms to the IRA.

At the other end of the pew, looking straight ahead, were Moynihan and his wife, who returned to Washington immediately after the service.

The crowd of 2,500, most wearing something green, applauded again when rector Msgr. James F. Rigney said in his homily that "governments of several nations, including our own" should help resolve the Ulster question.

He announced that St. Patrick's Cathedral had set up a Fund for Peace and Justice in Ireland, to be used "in as many nonviolent ways as possible" to reconcile the Catholics and Protestants there.

The thousands of spectators jamming Fifth Avenue eight and 10 deep--as numerous as usual, according to observers--seemed just as divided as Northern Ireland over the meaning of Flannery's presence, Cooke's absence and their own participation in six hours of festivities.

The cardinal's boycott didn't bother Margaret Butler of Woodside, N.Y., bundled up against the cloudy, 50-degree weather. "He made it political. He should have kept his mouth shut," she said. "No one is in favor of violence."

"Flannery will be the one grand marshal everyone will remember," said Rep. Mario Biaggi (D-N.Y.) as he took the absent Moynihan's place hosting a traditional breakfast feast at Charley O's Bar & Grill. "At least it will focus attention on the human rights problem in Northern Ireland."

Mayor Edward Koch, wearing a heavy white Irish wool sweater against the chill, took his share of catcalls as well as cheers. Earlier, he said he would march against Flannery. The IRA, he said, is "vile and despicable . . . they are not going to hijack this parade."

Although 3,800 police kept rowdyism to a minimum, five people were injured, none seriously, when a New Jersey man drove a small pickup headlong into the parade for 10 blocks and slammed into two cars. The driver was arrested and charged with driving while intoxicated.