By 1964, "Wagon Train's" script "consists of bits and pieces from all only-good-Indian-is-dead-Indian stories ever done."

1912, Sep 18   The Washington Post - Governor Wilson becomes a "Good Indian" -- "however, that he was not a consequence as 'a dead Indian.' " Cultural appropriation was added to the equation when the term was applied to a mans election to a group called "Tribe of the Sioux," -- "a municipal organization - and publicly initiated. 

          The Governor then said: "On the sacred tomahawk and pipe, I solemnly and sincerely promise and vow that henceforth and forever I shall endeavor to be a 'good Indian' whether successful or unsuccessful in the quest of moose or any other game, and that no matter how exalted my situation in life I shall neglect no opportunity to contribute to the welfare of the Tribe of the Sioux." 

I gotta say... this is weird but very common. From the 1770's until the 1970's, white adults "playing Indian" with others in secrete and public fraternal organizations -- all while, some of these prominent men were somehow tied to real indigenous people -- is mind-boggling. It's almost important to note that during this time, the extinction of actual American Indians, was expected. Many of these fraternal groups thought they were preserving a culture that they were also killing. 

Lastly, it does not say who this Governor Wilson is - but I am assuming it is Woodrow Wilson, governor of New Jersey, who won the Presidential campaign - as a Democrat - that following November. 

1912, Sep 18   The Washington Post 

1927 article pertaining to the phrase, that of course lays blame on the Indian by saying that their manner "of killing was so harrowing." But it also says that the phrase became pretty common.

1927, Jan 7   The Chehalis Bee Nugget   -- "Good" Indians -- The expression, "the only good Indian is a dead Indian," is said to have originated about the time of Grant's peace policy toward the Indians. In the enlisted personnel, a great number of men were against this policy, because the the Indians' manner of killing was so harrowing. A statement was made to the effect that among the Indians there are some good Indians, and a reply that was repeated from one man to another was that "The only good Indian is a dead Indian." There seems to be no record of the person who first made the remark.

1927, Jan 7   The Chehalis Bee Nugget 

Here's another interesting article from 1937 that blames the "bad Indian" behavior on "firewater."

Source: 1937, Nov 25   Kingsport Times 

"GOOD INDIAN" -- "The old-time Indian fighter used to wax profane as he declared that "the only good Indian is a dead Indian." Probably, considering the frequently barbarous treatment which the white man had inflicted for a few hundred years upon his red brother, the fighters didn't come across many examples of  "good" -- that is, docile -- Indians. And of course the same remark has been made about a good many other races, with as little reason.
          Now comes J. Allison Moore, special agent of the United States Indian Service in California, to say that the so-called "bad" Indians are made so by "firewater."
          "I have yet to investigate a single crime committed by an Indian who has not been influenced by alcohol," Mr. Moore recently declared. "The crime rate among Indians varies in direct proportion to the amount of liquor they get."
          Pointing out that disposing of alcohol to an Indian is a penitentiary offense under federal law and is a crime in most states, he said:
          "Only a thin veneer of civilization is present in the Indian's make-up. Give him a drink or two and he reverts to his savage type and performs acts of violence. The white race has been civilized for hundreds of centuries, and its members have been consuming alcohol for at least 2,000 years. We are accustomed to it, but the Indian is not."
          Even so -- as dome of our "dry" friends will arise to inform us -- liquor turns many ordinarily peaceable men into bad actors on occasion, without the slightest reference to whether their complexions are copper or white. - Johnson City Press 

"THE ONLY GOOD INDIAN 
IS A DEAD INDIAN"

from the How it Started column by Jean Newton

1946, June 29.   Asbury Park Press 

          General Phillip Sheridan, noted cavalry commander in the Union forces during the War Between the States, is the author of the line traditionally quoted as "The only good Indian is a dead Indian." Actually this is not the precise language used when this Americanism was born, but it is the popular version about which one of our readers inquirers. Here is how it started.

1937, Nov 25   Kingsport Times 

     After Custer and his band were ambushed and massacred*, the United States determined to take measures which would keep the Indians in hand. To General Sheridan was assigned the project of suppressing the red man's raids and restricting him to the reservations provided under treaty with Uncle Sam.          To this end, in January 1869, at Fort Cobb in the Indian territory, now Oklahoma, Sheridan held a conference with the chiefs of the Cheyennes, Comanches, Arapahoes and many other Indian tribes. "The Great White Chief," as Sheridan was called, made an address, and when he finished, each of the Indians chiefs answered. One, the head of the Comanches, Chief Toch-a-way, prefixed his reply with an attempt at ingratiation. 
          "Me good Indian," he said.
          To which Sheridan retorted: "The only good Indian I ever saw were dead.:" 

1946, June 29.   Asbury Park Press 

I need to make a very important notation: * George Custer wasn't killed until 1876, seven years AFTER Sheridan is said to have made this comment. Like many history articles from then - and even today - the facts are wrong and it changes the entire story.

In 1964, the phrase is embedded into many Hollywood movies.. mostly from all the anti-Indian Westerns that were popular for many decades.

1964, March 29   The News Herald 

The above TV listing says: Much time is spent talking about the 'blood moon' which is causing the Indian trouble on Wagon Train. But the main trouble comes from the script, which consists of bits and pieces from all only-good-Indian-is-dead-Indian stories every done. A superficial examination of prejudice on the frontier, with a lot of stock footage Indian fights.

Storyline
When Coop brings Kim Case to her home town of San Saba, he finds the people there in fear after recent Indian raids, and the nearby Army fort ready to attack. Army Major Starbuck's adopted son, Lance Starbuck, an old friend of Coop's, is an Indian himself whom Kim has long been in love with despite the strong opposition of her uncle, whose wife and children were killed by Indians. It is learned that the Sioux have teamed with the Crow and Kiowa to fight under Comanche Quanah Parker in retaliation for massacres led by notorious anti-Indian leader Santiago Quesada. Parker lays a trap for the Army and also attacks the wagon train stealing a wagon of rifles.