No. There is no single individual who won 49 Pulitzer Prizes, but some newspapers and news organizations have accumulated many for journalism categories over the years.
The Associated Press (aka AP), which is not a newspaper but a "wire service" (or news bureau) that supplies articles and photographs to newspapers won 49 Pulitzer Prizes. Most of the their awards were for photography or photojournalism, and the majority of their wins were prior to 1990.
The New York Times has an impressive record of 109 wins since 1917, the greatest number of Pulitzer Prizes won by one organization, as of 2011.