They say the new evidence allegedly ties Richard Thomas to the July 1996 attack.
The DA says the woman and her husband were awakened by an intruder in their Far Rockaway home. He threatened them with a gun before raping the wife.
If convicted, Thomas could face up to 25 years in prison.
Thomas is serving a 50-year sentence for sex assaults on a 12-year-old girl in 2004 and on a woman in 1996. Both cases were solved through DNA.
Defense attorney Scott Davis declined to comment on Monday.