Japan Times Archives (Library subscription)
Publication Date: 1897- 2017
The Mainichi website in English has a search function, which seems to go back one year.
Japan News (Yomiuri Shimbun)
Selected articles from 1989-present are available in Nexis Uni.
The Japan News website only goes back 30 days.
AJW: Asia and Japan Watch (Asahi Shinbun)
Their AJW website has news in English going back approximately 1 year. Non-subscribers are limited to 10 articles/month.