The Manhattan Project was a research and development project that produced the first atomic bombs during World War II. Stefan Kriege knew about it, and knew the Americans were close to success. (The first major test took place on July 16, 1945 when Trinity was detonated)
In the historical timeline the project ran from 1942 to 1946. But it is unclear how it faired in the New Order timeline. Stefan is likely referring to the later half of the research between 1944-1945. Wolfenstein takes place after February, 1945.
In 1939, Albert Einstein signed a letter to President Franklin D. Roosevelt noting German advances in physics and warned of the real possibility of the Nazis developing a uranium bomb. This lead to a race between Americans and Germans to be the first to create the bomb. B.J. would attempt to stop some of this research (on plutonium bombs) at a secret research base in Scandinavia.
Behind the scenesEdit
As the US already had Nuclear technology by 1945 in Wolfenstein (2009), it's unclear why they didn't use it on the Nazis. The Nazis don't start using nuclear weapons until 1948. The only detail mentioned in the Trailer concerning US atomic bomb making is that the "They beat us to the bomb, no one knows how..."
However, one possible reason the information in Wolfenstein wasn't taken into account, it is possible that very little of Wolfenstein (2009) was utilized as part of plot of Wolfenstein: The New Order. "...we asked him if the last Activision Wolfenstein game had any baring on their version to which he replied, "No it does not. We try not to include that game as part of our story. Personally, I think that Activision did a crap job."  In fact the designers claimed to be more of a fan of the original game in the series instead (Wolfenstein 3D).