Bonds, in an interview with MLB.com published Monday, said "without a doubt" he belongs in the Hall. He is eligible for the first time when the Baseball Writers' Association of America votes at the end of this year. Any electees will be announced in early January 2013.
When told of Bonds' comments and asked his opinion, Baker said Tuesday: "I agree with that. This guy was the best guy of his era. Big time."
Baker, who was Bonds' manager from 1993-2002 in San Francisco, said it never has been proven that Bonds used performance-enhancing drugs.
"If he did and they proved he used performance-enhancing drugs, then you have room for argument," Baker said. "But I don't think it's ever been proven. You know what I mean?"
On Nov. 15, 2007, Bonds was indicted for perjury and obstruction of justice based on his grand jury testimony in the federal investigation of BALCO (Bay Area Laboratory Co-Operative). The case against Bonds went to trial in March 2011, and on April 13, U.S. District Judge Susan Illston declared a mistrial on three charges that Bonds made false statements when he told a grand jury in December 2003 that he never knowingly received steroids and human growth hormone.
Bonds was convicted of obstruction of justice for one evasive answer about whether he received drugs that required a syringe and later was sentenced to 30 days of home confinement, two years of probation and 250 hours of community service.
Bonds won two MVP Awards with Pittsburgh before signing as a free agent with the Giants prior to the 1993 season.
"He was great before he got to San Francisco," Baker said. "When he got to San Francisco, he took it to another level. It was unbelievable watching this guy play every day. Not just hitting. He was the best baserunner. He was the best left fielder. He knew what was going on on the baseball field all the time. I mean all the time. Nothing ever surprised him. Ever."
Other players eligible for the first time in 2013 include Roger Clemens, Craig Biggio, Mike Piazza, Sammy Sosa, Kenny Lofton, Julio Franco and Curt Schilling.
"There's going to be a lot of discussion on Hall of Famers next year, probably more than any time in the history of the game," Baker said.