Going back to the days before the Yankees existed, the city’s best season of the 19th century came in 1889, when the Brooklyn Bridegrooms (later the Dodgers) of the American Association and the Giants of the National League combined for a winning percentage of .669. The Giants went on to defeat the Dodgers in an interleague championship that was a predecessor to the modern World Series.
Unfortunately, the files are not entirely complete. The statistics of many black leagues are now recognized as having been the equivalent of other major leagues, but the records are not comprehensive enough for accurate inclusion. A great season came in 1947, when the New York Cubans, with Minnie Miñoso and Luis Tiant Sr., won the Negro World Series after posting a .687 winning percentage, while the Yanks, Giants and Dodgers went are combined for a record 0.589. But the average winning percentage this season is dragged down by the New York Black Yankees, who were an abysmal 12-43.
Keeping a high winning percentage with multiple teams involved is tough. Fittingly, New York’s best baseball season, dating back to the founding of the Giants as the New York Gothams in 1883, technically came in the dark four years after the Giants and Dodgers headed to the West, which left the Yankees as the only game in town. It was 1961, the Mets were a year away from stumbling, and the Yankees posted a .673 winning percentage as Roger Maris and Mickey Mantle battled to break Babe Ruth’s home run record. They put the icing on the cake by winning the World Series.