The latest rumors are that the 49ers are willing to trade Harbaugh at the end of the season for a draft pick, and two teams have jumped to the front of his race: the Oakland Raiders and New York Jets.
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That being said, lets say the Jets were a serious player here. Harbaugh probably would want a say in personnel matters, meaning that either John Idzik or the new Jets General Manger would have to be willing to let the coach have a major say in the decision making process. That is unless Woody Johnson decides to give Harbaugh the keys to the entire operation, GM and Head Coach.
Harbuagh is a winner, even with all the problems in San Francisco. He took a downtrodden 49ers franchise and took them to the NFC Championship game and a Super Bowl appearance in his first three years by the Bay. He's a former quarterback, which would be a plus for a team that needs an offensive minded head coach.
That being said there have been numerous stories that the 49ers' players have been unhappy with the strict nature by which Harbaugh runs the team. A lot of people find him too abrasive and too much of a high-wire act. It is fair to wonder if his bristly personality would work well in New York. History tells out that it took Tom Coughlin years before he shed his bristly personality, and when he did the Giants won a Super Bowl. Al Groh, was a head coach with a rough personality that was run out of the New York when the Jets players rebelled on him in 2000.
While landing Harbaugh sounds like an attractive option, it may not be the best option for the Jets.