Obama recognized the NFL champions Thursday during a White House ceremony on the South Lawn.
"That whole story got blown a little out of proportion," Obama said of the so-called "deflategate" investigation as the crowd chuckled.
Continuing to honour sports teams for their community service, Obama thanked the Patriots for visiting hospitals and schools in New England and wounded veterans at Walter Reed Medical Center. He said team members ran in this year's Boston Marathon and raised more $230,000.
Obama joked that he wished the city of Boston would share some its sports titles with his hometown of Chicago.
"I'm hoping that I get to see the Bears before I leave here," he said.
Patriots owner Robert Kraft presented Obama with a Patriots jersey and signed helmet. He called the president the "ultimate Patriot," despite his allegiance to his beloved Chicago Bears.
Secretary of State John Kerry, Sen. Elizabeth Warren of Massachusetts and Sen. Angus King of Maine were among the crowd cheering the champions.
The Patriots' 45-7 victory in the AFC title game was marred by accusations that a team employee had partially deflated game balls, making them easier to catch and throw. A league investigation is ongoing.
The Patriots defeated the Seattle Seahawks 28-24 in this year's Super Bowl. It was New England's fourth NFL title in 14 years.