The developer called them visionaries. Theo Ellington was among them, the pioneering home buyers who took a chance on the new condominiums at the old Hunters Point Naval Shipyard, a weed-choked, 420-acre Superfund site that had been largely fenced off since the mid-1970s.

Ellington, who grew up nearby at Third Street and Palou Avenue in the Bayview neighborhood, had bid on other properties but always lost out to other buyers. Jason Freed was another. A consultant for environmental groups, he managed to buy a unit just as his landlord in the Haight was selling his apartment.

Both Freed and Ellington were able to buy one-bedroom condos for less than $500,000, unheard of in a city where condos now average nearly $1.2 million. They moved in 2½ years ago.

“I literally rubbed my pennies together,” said Ellington, who recently left his position as community relations director of the Golden State Warriors to run for District 10 supervisor. “The timing was perfect, because this was the last affordable place to live in San Francisco.”

Freed said “the Shipyard was the only thing in my price range.”

In some ways, the high hopes these two men had for the San Francisco Shipyard development are taking shape. In the evening, Ellington and Freed — with their dogs Leroy and Grant — join other residents in the grassy pocket park overlooking the bay. They shoot the breeze while their dogs play and the last of the sun strikes the glass towers off in the downtown distance. The hilltop community is starting to feel like a neighborhood.

“It’s all walks of life — folks who grew up in San Francisco, folks who moved here for jobs, folks starting families,” Ellington said. “There is a calm and serene feeling you get up here.”

But over the past few months, residents say, that sense of calm has been broken by the alarming news that the cleanup of contaminated soil on the site might have been botched. That opens the possibility that poisons remain from the time the shipyard was home to the Naval Radiological Defense Laboratory from 1946 to 1969, when tests were conducted to determine the effects of radiation on living organisms and ships contaminated by atomic bomb explosions were dry docked at Hunters Point.

In January, the Navy released a report stating that half the soil testing performed by Tetra Tech, the engineering firm that was paid more than $350 million to clean up the shipyard, was flawed. Then this month, an environmental watchdog group released a letter written by John Chesnutt, manager of the EPA’s local Superfund Division, that stated as much as 97 percent of Tetra Tech’s cleanup data from two parcels on the site was suspect and should be retested.

Tetra Tech responded that both conclusions are inaccurate. The Pasadena environmental engineering firm, which has a market capitalization of $2.85 billion, said it would pay for retesting.

“We believe that any concerns can be directly addressed by actually retesting and analyzing the areas in question,” Tetra Tech CEO Dan Batrack said. “We want the Hunters Point community and the Navy to know that Tetra Tech stands by its work at Hunters Point.”

The Navy and the regulatory agencies overseeing the cleanup have always insisted that parcel A, where the condos Ellington and Freed live in were built, was never contaminated. The land was home to barracks and not used for the radiological testing or other industrial uses that spread contaminants across other parts of the facility, according the Navy. Also, Tetra Tech did not do the testing at parcel A.

But some San Francisco Shipyard residents say given the uncertainty surrounding Tetra Tech’s work, any retesting should include parcel A. Developer FivePoint is building 1,600 homes on the 20-acre hilltop site. About 300 units have been completed, and another 150 are under construction. When completed, the San Francisco Shipyard will contain 10,500 units of housing.

“Someone needs to provide reassurance and certainty that parcel A is OK,” Ellington said. “I think you will see the residents come together to ask for parcel A to be retested. There is too much at risk not to provide the level of certainty that the community deserves. A lot of folks have lost confidence.”

Freed said that soil samples should be taken as soon as possible before the remaining land is filled with concrete foundations.

“If you have the people and the equipment coming out here to retest, you can’t tell me it would cost that much or take that much longer to do parcel A, too,” Freed said.

Longtime neighborhood residents have a conflicted and complicated relationship with the development. Many like that one-third of the housing will be affordable. Others like the new artists studios, 300 acres of parks, planned grocery and other retail, the office and biotech research space, the coming schools and 120-room hotel, all of it providing local construction jobs

The other view from the working-class neighborhood is that the luxury housing at the San Francisco Shipyard will eventually weaken the Bayview’s African American culture, fuel gentrification, and widen the division between rich and poor. Townhomes sell for $1.4 million.

And the allegations of shoddy testing also underscore the health concerns Bayview residents have raised for decades. Hunters Point neighbors have long blamed pollution from the shipyard for the neighborhood’s cancer clusters, and high rates of asthma and heart disease.

At a San Francisco Planning Commission hearing Thursday that focused on changes to the development plan, Bayview native Carolyn Scott, whose father worked in the naval shipyard, said generations of people in her family have suffered from suspiciously aggressive forms of cancer and asthma. She said that all the women in her family have had multiple miscarriages — she herself had 10.

But she said the vision for the San Francisco Shipyard — the city’s biggest development — is still a vital one.

“I am concerned about (the health issues), but I am also looking at the hope and opportunity that project has for the community,” she said. “Out of a mountain of despair comes a stone of hope.”

Supervisor Malia Cohen, a Bayview native, said that while the new residents of the development are “raising most of the questions,” for older people in the Bayview “it’s a moment of ‘I told you so.’”

“It’s a moment of vindication — all their protests and shouting and fears were basically dismissed by previous administrations,” said Cohen, who has called for public hearings on the cleanup scandal. “My role is to say ‘You were right, now let’s correct the record and move forward.’”

Linda Pennington, an African American woman from New York who had previously been living in Monterey Heights, bought a home at the development largely because she wanted to live in a neighborhood with a vibrant black culture.

She has not been disappointed. She frequents Radio Africa on Third Street on Tuesdays for community night. She eats at the Old Skool Cafe, a nonprofit soul food supper club on Mendell Street, and rarely misses the lectures or jazz performances at the Bayview Opera House.

“I felt good about coming to a historically African American neighborhood, and all the things that I was hoping for have exceeded expectations,” she said.

But while she has immersed herself in the Bayview that lies outside the development, she worries the new neighborhood has not yet been successful integrating into the area. It’s not a place where a lot of residents in the Bayview, which includes some of the poorest precincts in the city, feel comfortable, she said. People who don’t live or work in the San Francisco Shipyard rarely hang out at its pocket parks or shop at the the Storehouse, the one convenience store on the property.

There have also been a couple of disturbing incidents. One afternoon, a development resident called the police to report “suspicious” high school-age boys walking through the neighborhood. It was Pennington’s African American son and three friends from the San Francisco School of the Arts — two were white and one was mixed race.

“We take these things in stride in my family, but the mom of my son’s friend was really upset. She asked: ‘Why would they assume that these kids don’t belong over there?’” Pennington said. “The reality is that it doesn’t feel integrated. The vision I had in mind was not one where people are separated. I feel more needs to be done to break down economic and racial barriers.”

On a recent walk around the development, Ellington ran into Vermar Langley, an old pal from nearby Gloria Davis Middle School. Langley is a plumber with Local 38 and is working on some of the townhomes under construction.

“This was my dream when I was a little boy, I wanted to be working in my neighborhood and I’m doing it,” Langley said. “I grew up 30 seconds away from here and watched this place growing up. We always heard ‘Hey, they are going to be redoing the shipyards.’ Ever since we were in middle school it’s been talked about. Now it’s finally here, and I’m working here. It’s a dream come true.”

Langley said he hopes to be able to afford a unit at the development some day. “Until then, I’m living in Pittsburg,” he said.

Ellington said the promise of the San Francisco Shipyard is that someone like Langley could end up living in a new home on the hill.

“Those are the stories we need to be able to tell, people from the community who can not only work here but live here as well,” he said. “Unfortunately at the moment, the whole fake soil sample thing is kind of disrupting the dream.”

J.K. Dineen is a San Francisco Chronicle staff writer. Email: jdineen@sfchronicle.com Twitter: @sfjkdineen