Peltier has NOT been adopted as a prisoner of conscience by Amnesty although they have expressed concern about the fairness of the proceedings leading to his conviction.

The organization has called for his release on parole, one of its concerns being that his extradition from Canada in 1976 -- where he had fled following the shootings -- was secured on the basis of coerced testimony from someone who later retracted it but Amnesty accepts 'the fact that appeals before the courts have long been exhausted'
(There have been several appeals since the original conviction, I'm sure our resident expert can confirm the actual number.)

Amnesty International has additionally called on prison authorities at the Lewisburg Federal Penitentiary to improve conditions for Peltier AND other inmates held in isolation at the facility for prison disciplinary violations. Peltier did escape for a time in 1979 and, according to a Huffington Post article, following the parole refusal in 2009, he also has had numerous infractions in prison, some of them drug-related.

Although Amnesty only supports his parole, unsurprisingly, it is the official well funded site (linked by Jeri) that makes an argument for Peltier's innocence. Unremarkably, there are other sites that make an equally convincing argument for his guilt but it is not my intention to barrage everyone with links they can look up themselves.

Inasmuch as it is not realistic to impart to the murdered FBI Agents Coler and Williams the historical guilt and culpability for broken treaties between American Indian tribes and the U.S. Government it's also equally unreasonable and very misleading to give Peltier the status of 'representative' of all the disposed Native Americans.
There are American Indians like Paul Demain who have investigated the issue of "without doubt," and state "it makes me angry to think we have all been used. But, I can't be afraid to say the King has no clothes."
The Independent Native Journal article

Although questions about the government's handling of the Peltier prosecution has provided fuel (and profit) for writers and film producers who have sought to turn Peltier into a 'political martyr' Harvard law professor Allan Dershowitz, a defence lawyer with liberal political leanings, was moved to describe Matthiessen's book as "utterly unconvincing" and "embarrassingly sophomoric when he pleads the legal innocence of individual Indian criminals.