Craig Spencer's apartment in Harlem has been sealed off and authorities are trying to track down those who came into contact with him in the days before he was admitted to hospital.
The 33-year-old, originally from Detroit, Michigan, had been working in west Africa for medical charity Doctors Without Borders.
Speaking after the announcement, New York Mayor Bill de Blasio said there was no reason for people to worry.
He told a news conference: "Ebola is an extremely hard disease to contract. It is transmitted only through direct contact with infected persons' blood or other bodily fluids.
"Travelling on the same subway car ... does not ... put someone at risk."
Mr Spencer returned from Guinea more than a week ago but reported coming down with a fever and diarrhoea on Thursday. He has been held at an isolation ward at Manhattan's Bellevue Hospital, a designated ebola centre.
Two friends and his fiancee who he was in close contact with were placed in quarantine and one remains in hospital. A fourth person, a taxi driver, did not come into close contact with Mr Spencer.
Guinea is one of the three worst-hit countries in the latest ebola outbreak, along with Sierra Leone and Liberia. Nearly 4,900 people have died so far.
Mali had earlier become the latest country to admit one of its residents had tested positive for the disease. A health ministry official said the girl had just arrived from Guinea, where her mother died of the virus a few weeks before.
Meanwhile, the World Health Organisation says Ebola remains a global emergency, and it's still trying to slow the rate of new infections.
However, experts are 'reasonably confident' the virus isn't spreading to the countries surrounding those most affected in West Africa.
The number of recorded cases of the disease has reached nearly 10 thousand with almost 5,000 deaths.