Stephen "Greg" Fisk was found by his son on Monday, just weeks after taking office. Results of an autopsy are expected within days.
Police have dismissed rumours that he was assaulted as "speculation" and said there was no evidence of forced entry.
Fisk defeated the incumbent, Marrill Sanford, in October's mayoral elections.
The Juneau Police Department said in a statement: "Detectives are actively investigating facts of the incident, and all evidence is being preserved and documented."
Police Chief Bryce Johnson told a local newspaper that an attack is "one of the possibilities out there, but there's others that could have happened".
"There could've been a fall. There's lots of things that would cause it."
Mary Becker has been named acting mayor in light of the 70-year-old's death.
Juneau is the state capital of Alaska and has a population of 32,600 people.
"This was a terrible day for all of Juneau," said Jill Ramiel, president of the Downtown Business Association.
"He was never afraid to say what he thought."
Fisk's campaign chairman, Bob King, added that "for that potential to be snuffed out is just a crushing loss".
The newly elected mayor of Juneau in Alaska has been found dead in his home and police are investigating the cause.