/u/mikedash wrote the article on Shakushain, the most famous chief who revolted against Clan Matsumae in the late 17th century in: "The Octogenarian Who Took on the Shoguns (Smithsonian.com, June 20, 2013", with some further readings in English at its end.

You can begin with some of the references listed there (I'd also recommend Brett Walker's The conquest of Ainu Lands as the departure point of reading in English).

[Added]: Alternatively, you can also check the following excellent previous posts (and especially its sources) on the relation between the Ainu people and the Japanese in this subreddit:

• What were Japanese/Ainu relations like before Hokkaido became part of Japan? : answered by: /u/mikedash
• Was there any significant Ainu involvement during the Sengoku Jidai? : answered by: /u/ParallelPain
• My previous post in Looking for reading suggestions on Hokkaido during Muromachi / Sengoku periods also have some links to the English articles authored by a few museums in Hokkaido.

One of my favorite books that I own is Harukor by Honda Katsuichi. It is an incredibly informative book about Ainu culture and history. There is also another interesting book I would recommend called "Our Land was a Forest". Other than that I don't know how to help, as the majority of information on this subject is either in Russian or Japanese.