A third man swam to shore.
Searchers, including state, local and U.S. Park police, searched by boat, foot and helicopter for Barrett Raymond, 31, of Hyde Park, N.Y., and Baylin Coddington, 26, of Millbrook, 15 miles east, Hyde Park Police Chief Eric Paolilli said.
Searchers focused on an area just west and north of Roosevelt's Springwood estate in Hyde Park, now a national historic site, where the canoe with Raymond, Coddington and Michael Maurer, 29, of Hyde Park, overturned around 1:30 a.m. Friday, police said.
Maurer, who reached shore, called for help from an apartment complex, police said.
He was taken to a hospital with hypothermia but suffered no serious injuries, police said.
Paolilli said the search, covering 3 miles north and south of a boat club on the river's east bank, was still in rescue mode, even though the Coast Guard formula for surviving in 48-degree water was 8 1/2 hours.
The three men's canoe excursion started around 11:30 p.m. Thursday about 3 miles north of the Roosevelt site, near the Vanderbilt Mansion National Historic Site, police said. The mansion is named for railroad executive Frederick W. Vanderbilt, grandson of shipping and railroad magnate Cornelius Vanderbilt.
Paolilli said police were trying to determine why the men were on the river and how the canoe flipped over.
"We have no reason to believe there's any criminality involved," he said.
Hyde Park, just north of Poughkeepsie, is about 90 miles north of New York City.