Cavendish's current employers, HTC-Highroad, will no longer be competing at the end of the current season, leaving the 26-year-old with a decision to make over his future.
"I hope so," Thomas replied when asked by BBC Sport about the possibility of Cavendish signing for Team Sky.
"He has proved he's the fastest in the world and to have him in the team would be amazing. To lead him out, week in week out, would be special."
Cavendish and David Millar were the only members of the eight-strong British team in Copenhagen who do not ride professionally for Team Sky.