The Pride of Baltimore, the replica of a 19th century Baltimore clipper that had been the object of a three-day search, sailed safely into Delaware Bay yesterday after weathering storms at sea. Then it ran briefly aground late last night.

Once again afloat, but leaking from damage suffered in pounding against a shoal in windswept Delaware Bay, the 90-foot schooner was reported at 2 a.m. today waiting to be towed or escorted to Wilmington, Del. No injuries were reported.

The handmade, $475,000 schooner was at anchor in the bay shortly before 11 o'clock last night when it was driven against the soal, about 10 miles west-norhtwest of Cape May, N.J., and started taking on water.

"It sprang the planks," said Tom Norton, director of Operation Sail, which leases the Pride from the city of Baltimore. He said caulking came out of the seams which began to leak. The full extent of damage was unknown.

With the aid of the schooner's own pumps and one dropped from a Coast Guard helicopter, the captain and 10-member crew freed it from the shoal and were reported "keeping up with the water."

Despite "nasty" weather, with 20-knot winds driving 6-to 8-foot waves, the wounded "Pride" was in no danger of sinking, the Coast Guard said.

"I just can't believe this happening after all she's been through," said Norton, who during the height of last night's uncertainty expressed fear that "we could lose her."

"She's not rigged for this kind of weather," said Annapolis shipbuilder Melbourne Smith, who directed the ship's construction. "It's a delicated little boat and should never have come up this far so early."

Concern for the vessel late last night followed rejoicing earlier yesterday when the schooner, longsought and storm-tossed, finally re-established radio contact with the shore.

The Pride, which had failed to arrive on schedule in Norfolk last Sunday, had been blown 200 miles off course, her crew said. She suddenly emerged yesterday from days of silence heading toward the Chesapeake-Delaware Canal, on her way home.

"They called us around 3:20 and said their radio antenna had been knocked out," said Mike Bayones, a radio dispatcher at the Coast Guard's Cape May station.

Bayones said he spoke with the captain, Charles Whitcomb, 52, of Cambridge, Md., over the ship's short range radio for several minutes.

"They said they had heard the Coast Guard broadcasts but hadn't been able to contact us until they were at the entrance of Delaware Bay. They said they had gotten blown off course after going through two storms," Bayones said.

Later reports from the vessel indicated some damage to the sails, and damage to one of the small boats onboard. No injuries were reported, but Whitcomb said the ship was running short on food.

Besides Whitecomb, the crew consists of eight men and two women between the ages of 19 and 28. Most of the crew members are from the Baltimore area.

Yesterday afternoon, a Coast Gurad spokesman in Portsmouth, Va., said the service was "very happy" that the ship had turned up safely, despite the filure of a major, three-day search involving a computer, sailing and navigation experts and six long-range military planes that had combed thousands of square miles of ocean from Cape Hatteras, N.C., to Cape May.

"We can't say we're the perfect searchers," the spokesman said after the Coast Guard failed to find the Pride of Baltimore.

The 90-foot topsail schooner embarked from Wilmington, N.C., last Thursday on the way to Norfolk.

According to Whitcomb, who talked by radio late yesterday with Baltimore Mayor William Donald Schaefer, the ship encountered the first storm the next day, 100 miles off Cape Hatteras.

The sleek, fast-running schooner, capable of sailing at up to 12 knots, headed out to sea, Whitcomb said, but was blown substantially off course when it was struck by a second storm.

By Wednesday, the Pride was 250 miles off the Delmarva Peninsula, according to her captain. The Coast Guard, notified by a Norfolk city official, started to search for the overdue vessel, but limited its efforts at first to an area only 40 miles offshore.

The two-masted schooner is equiped with a radio with a 30-mile range, and a small, 85-horsepower motor used for docking. It does not have emergency signaling devices carried by many ocean-going yachts, officals said.

Once the second storm died on Wednesday, Whitcomb said, the Pride was able to pick up enough easterly wind to sail back toward shore.

"I'm sure there were some seasick people," said Thomas Gillmer, the Annapolis naval architect who designed the Pride-the only authentic Baltimore clipper in the world.

"I feel she's a good, strong seaboat, but a little tricky to sail. They've changed captains three times in six months and I guess that was the only thing that worried me. Nobody's sailed one of these things in 100 years."

By Thursday, the Coast Guard had expanded the search area from Cape Hatteras to Chincoteague and extended it to 180 miles offshore using two long-range planes equipped with radar.

Yesterday, their search intensified.

Using a computer with data on winds and currents, the service pinpointed an area 280 miles northeast of Cape Charles, Va., as a "highly probable" spot to look.

Six aircraft, including two Navy submarines spotters and four Coast Guard, Marine and Air Force planes from as far away as Florida, were called in.

The large area was divided into six sections. The planes, flying at varying altitudes with 8 to 10 men onboard, started at one end of each square and methodically criss-crossed the area. The planes are able to stay airborn for 6 to 8 hours, a spokesman said. Besides radar, the men visually scanned the water, which a coast guardsman said yesterday was "exhausting work."

The Coast Guard searches were called off at night, when the Pride apparently was headed toward the coastline.

The ship was hand built in Baltimore's Inner Harbor and launched in 1977 as a floating monument to the city's maritime history.

It has been on a commercial cruise in the Caribbean since last October and is scheduled to leave for Canada next month.

Yesterday, the DuPont Co. of Delaware and the goddard Space Flight Center in Greenbelt offered to pay for sophisticated electronic equipment for the vessel. A transponder, a device that would allow the space center to locate the Pride by satellite at any time, will be installed, Mayor Schaefer said.

Baltimore officials have said this week they hoped to buy a long-range radio telephone for the Pride, and DuPont said yesterday it would pick up the bill.

When fully rigged, the Pride carries seven sails and has a total sail area of 9,523 square feet. Its top speed of 12 knots, characteristic of the sleek Baltimore clippers, is considerably faster than other ships her size.

There are two trapezoidal mainsails rigged on her two main wooden masts; a triangular jib and staysail ahead of the forward mast; two square rigged sails bent ot yards on her forward mast and a small triangular topsail above her mainmast.

Although the vessel has no shower, no refrigerator and those aboard sleep in hammocks slung beneath the crossbeams, an official said yesterday there is a waiting list of 100 would-be crewmembers eager to go to sea on her. CAPTION: Picture 1, CAPT. CHARLES WHITCOMB . . . made radio contact; Picture 2, The Pride of Baltimore returned yesterday afer being overdue five days.