"Obviously, I'm disappointed to come that close," he said in a statement. "I feel for my family, the organization and the fans. Hopefully, next year."
Mike Piazza was next with 62.2 percent, up from 57.8 last year. Jack Morris was 78 votes short at 61.5 percent in his 15th and final appearance on the writers' ballot, a drop from 67.7 percent. Morris replaces Gil Hodges (63 percent in 1983) as the player with the highest-percentage of the vote not in the Hall.
Jeff Bagwell dropped to 54.3 percent from 59.6, and Tim Raines to 46.1 from 52.2.
Controversy over how to evaluate stars tainted by the Steroids Era continued to impact the vote totals of players with stellar statistics. In their second appearances on the ballot, Roger Clemens dropped from 37.6 percent to 35.4, Barry Bonds from 36.2 to 34.7 and Sammy Sosa from 12.5 to 7.2.
Bonds, baseball's career home run leader, is the only seven-time MVP in major league history. Clemens is the lone seven-time Cy Young Award winner.
"As for what they did, I don't think any of us will ever really know," Thomas said. "But I can just tell you, what I did was real and that's why I've got this smile on my face right now because the writers, they definitely got it right."
Mark McGwire, appearing for the eighth time, fell from 16.9 to 11 percent — down from a peak of 25.6 in 2008. Rafael Palmeiro will be dropped from future ballots after falling to 25 votes and 4.4 percent — below the 5 percent threshold necessary to remain eligible. One voter submitted a blank ballot.
"I can go home and sleep at night and rest," Thomas said, "so I don't have to worry about all the nonsense that the other people are going through, because I know I won't be getting a call in the middle of the night from someone saying, oh, he did this or he did that."