Thomas Hardy

Captain Thomas Hardy was the master of HMS Victory during the Battle of Trafalgar, and the flag captain of Lord Admiral Horatio Nelson. When Ben, Polly and the Second Doctor arrived onboard the Victory, they were taken before Hardy, who believed them French spies or deserters from another ship. It was only because the trio had captured the interest of Nelson that they were not dealt with more harshly. (PROSE: H.M.S. TARDIS)

Behind the scenes
Though the story never mentions his first name, it does identify him as Nelson's "flag captain", leaving little doubt as to his identity.