It was not exactly smooth sailing yesterday for the new owner of the presidential yacht, the Sequoia.

Thomas Aquinas Malloy, a Rhode Island businessman and home builder, held a news conference aboard the yacht he bid $286,000 for and said that he was "accepting the craft in protest" because much of the furniture had been removed. Among the items he wanted back was the Harry Truman piano.

Then, as Malloy prepared to watch the Sequoia float away from the Washington Navy Yard toward providence, where he hopes to start a national tour and charge visitors $2 apiece to see it, a snafu occurred that kept the yacht tied up at the dock an extra four hours.

One of the companies underwriting a $550,000 insurance policy wanted the Sequoia inspected to see if it were "seaworthy." As Malloy fumed and perspired, a ship surveyor from the United States Salvage Association, Inc. in Baltimore was dispatched to check out the 52-year-old vessel.

How did he know it was "seaworthy", Malloy was asked.

"It better be," he said in a loud voice, "I'll tell you that. Or I made a hell of a mistake. I've made 'm before, too."

The 51-year-old Malloy said he once bought a night club with a leaky roof that eventually burned down. He said he built condominiums successfully in Illinois and Florida, but unsuccessfully in Rhode Island. Recently he has been promoting concerts in New England and is head of a Florida holding company called Leisurecraft Corp.

A year ago he was almost killed when he fell asleep at the wheel of his car about 3 a.m. between Newport and his home in Cranston and hit a bridge abutment. He was hospitalized six months with a severe leg injury and is still on crutches.

And what did he hope to get out of the Sequoia?

"Money, I hope," he said, adding that he thought he could attract 750,000 persons to see it in one year, operate it as a museum for five years, "build up its value," and eventually turn it over to a museum, taking a tax deduction on it.

One of the first places he hoped to make money was later this summer at Newport during the America's Cup Races. He said he just wished he had all the dinnerware and furniture, much of which has been taken to Camp David. "They bring back the dining room table and they take the dining room chairs," Malloy said. "They bring back the bed and take the side piece. Even the wheel was gone for a while, bound for the Navy museum. But it was put back.

Unlike President Carter, who never used the yacht and ordered it sold as a cost-cutting measure. Malloy was anxious to move it out, if only Andrew Pierce, the surveyor, would arrive. He finally did, and pronounced the vessel "very nice," although he later conceded that it was "not built for the outside," meaning the open sea.

Lt. Keith Curtis, who would have been the commanding officer had the President kept it, took leave to command the yacht on its trip north. "Don't scratch the railing," said the new owner as the gangplank was lifted aboard and the Sequoia moved away from the Navy Yard for the last time.

"If it doesn't work as a tourist attraction," said Malloy's son Kevin "we can turn it into a floating disco."