While Chakravarty was given the award for the year 2012, Ghosh received it for the 2013.
At a ceremony at the Raj Bhavan here, Mukherjee said he felt honoured to present the award, which has been instituted in the name of eminent Bengali literary figure Sunil Gangopadhyay.
He said Gangopadhyay was a "path-breaking author" many of whose works he had himself read.
The research that Gangopadhyay did for his works, which are based on historical happenings, stood out among the contemporary literature.