TROUBLE is bubbling up once again over notorious, polluted Boston Harbor. Cape Cod activists and environmentalists are up in arms over a 9 1/2-mile ocean outfall tunnel, part of the 13-year, $6.1 billion Boston Harbor cleanup project.The new pipe will carry treated waste-water out beyond the harbor to be dispersed into the deep waters of Massachusetts Bay. Activists say treated waste water from the pipe will contaminate the marine life of the bay. "We're talking about things that do not dilute and that will wreak havoc on our sensitive ecosystem," says Etta Goodstein, a member of Stop the Outfall Pipe (STOP), a new organization dedicated to doing just that. "On Cape Cod, our environment is our economy." Ms. Goodstein and others are concerned about nitrogen content from waste-water discharge that could lead to algae blooms and red tides; contamination of Cape Cod beaches; and a plan to stop short of full secondary sewage treatment in order to cut costs. They believe these factors could threaten the area's two largest industries: fishing and tourism. Many are also concerned about about Stellwagen Bank, a rich fishing and whale-watching area 16 miles east of the discharge point. Last week, STOP and other groups staged a "blockade" of about 100 to 200 boats around the entrance of Cape Cod Bay to protest the outfall pipe. In addition, Goodstein, along with a group of STOP activists carrying signs, held a meeting in Gov. William Weld's office last week. One activist, attired in a lobster costume, added a few heated words: "I'm boiling mad about this pipe," he said. Governor Weld, who posed for pictures with the six-foot crustacean, expressed "solidarity" with the activists but would not support a halt to tunnel construction. Secretary of Environmental Affairs Susan Tierney assured the protesters that the state would not back away from full secondary treatment. Officials from the Massachusetts Water Resources Authority (MWRA), the agency created to oversee the harbor cleanup project, say the outfall pipe poses no danger. They say the discharge from the pipe will be sufficiently treated and monitored. "The water [from the outfall pipe] comes out swimmable. That's it," says MWRA executive director Paul Levy. "The idea that beaches are going to be polluted is pure garbage. It would be one thing if we were dumping sludge out there, but we're dumping water out there." The tunnel, which is already under construction, is scheduled for completion in 1995. Boston Harbor is considered the dirtiest harbor in the United States. The cleanup project, scheduled for completion in 1999, will include new primary and secondary treatment plants, two undersea tunnels totaling 14 miles, and a sludge-processing plant. For years, the harbor has been the dumping ground for industrial wastes and an estimated 450 million gallons of poorly treated sewage waste-water daily. Currently, 43 cities and towns in the Boston area send their sewage to the city's outdated treatment system; some of the pipes date back more than a century. The cleanup is being carried out as part of a 1986 court order issued when waste water discharges to Boston Harbor were found to be in violation of the federal Clean Water Act. The idea of cutting back on full secondary treatment has been a matter of considerable debate, since most of the project's cost will be paid for by homeowners and businesses located in the 43 Boston-area communities. Last year, homeowners paid an average annual rate of $400 for water and sewage costs, but that rate is expected to reach $1,200 per household in 1999, Mr. Levy says. There are also economic benefits. The project promises to pump $3 billion into the local economy and provide jobs for thousands of workers.