But in 1954, after a perfunctory excavation failed to find human remains there, the city chalked up the cemetery to local lore - and paved it over for a parking lot.
Decades later, that decision is facing renewed scrutiny from archeologists who want the city to dig up the plot yet again - believing bodies still rest where a complex is set to go up next year.
"I would urge that they take another look," said Queens College anthropology Prof. James Moore. He called the case an issue of "heritage, historic preservation and just simple respect for the dead."
The city Economic Development Corp. has dismissed the calls for excavation as thinly veiled attempts to halt construction of Flushing Commons, a mix of housing and retail on the site of the municipal parking lot.
An EDC spokesman, David Lombino, argued that opponents of the project - who fear its effect on small businesses and traffic - will jump on anything to stop it before a looming City Council vote.
"There are no plans to revisit that determination" of a nonexistent graveyard, Lombino said.
But a Daily News investigation has found the city Corporation Counsel's decision to deem the graves "nonexistent" on Feb. 3, 1954, may have been hasty.
A spokeswoman for the Law Department said that records of the excavation - two weeks of hand-digging in 1953 that did not turn up any bones - were "not readily available" last week.
The spokeswoman, Connie Pankratz, vowed to search in off-site archives in coming weeks.
The EDC insists the cemetery does not exist - though their officials cannot produce records showing how the Public Works Agency carried out the excavation.
"It's hard to say, without reading the  report, whether the hand-testing was adequate," said Christina Rieth, the state's official archeologist.
Moore and Rieth both argued that the modern means of finding graves - including ground-penetrating radar and topsoil stripping - would prove more reliable than hand-digging did in 1953.
They also noted that attitudes toward long-lost cemeteries were much less sensitive in the 1950s - an era before city laws on cultural resources and landmarks existed.
And they figured a lack of detailed record-keeping at the time has left many lingering questions about the 1954 designation.
The city declared the cemetery "nonexistent" despite 20th-century accounts of tombstones in the Brooklyn Eagle and Long Island Daily Press.
A 1950 story in the Long Island Daily Press even reported two specific burials in church records: "C. Silliman" in 1846 and "Hutson grandchild" in 1857.
A city report in 1988 indicated that some bodies from the Methodist graveyard were reinterred in Flushing Cemetery between 1853 and 1867.
A Flushing Cemetery superintendent, however, told The News last week that he could not find any records of the Methodist reinterrments - exposing another potential flaw in the city's stance.
Even if the exhumations took place, the 1988 report suggested at least 30 bodies were unaccounted for. They could still lie beneath the parking lot - and at the center of one of the most controversial projects in Queens.