Although I have never seen an official directive, I think it is safe to say that Niagaras were not regularly assigned to the 20th Century. That train was so special to the New York Central that it always received the best and most fashionable equipment. Both the Niagaras and the E7s were delivered in 1945. Thus once the E7s became available, they were the preferred locomotives to lead the 20th Century. That is not to say that no Niagara or no Mohawk ever pulled the 20th Century, just that those instances would have been very rare.
For support, just consider the photographic evidence. The 20th Century had to be one of the most photographed trains. I searched all my books about the New York Central and found only two photographs showing a Niagara on the 20th Century. One was a special case where severe winter weather in January 1948 had the train 3-1/2 hours behind schedule, likely because the E7s had been unable to cope with the deep snow. The other was June 1946 with a Niagara leading the 20th Century out of Chicago.
On the other hand, there are many photos with references about Niagaras pulling the Commodore Vanderbilt and the Advance Commodore Vanderbilt and other named limiteds. The other limited trains mentioned were the Empire State Express, Ohio State Limited, Knickerbocker, Laurentian, Chicagoan, Lake Shore Limited, North Shore Limited, Mercury, New England States, and many mail and express trains.
Modeling the NYC of the 1950s