While I agree with Michele that Clemens spent the bulk of his career with the Sox and had some of his biggest achievements there, he won his two World Series rings, his 300th game, and recorded his 4,000th strikeout wearing a Yankees cap. He has won his last 67 games with the Yankees (
124 60 games his first four seasons and 7 more so far this year). It’s been a long time since he wore a Red Sox unie and is now identified by most casual fans as a Yankee. More importantly, Clemens sees himself as a Yankee.
Generally, I’d say a player should have the right to choose his cap, with the HOF having a veto power over any obviously unreasonable choice. Clemens going in as a Yankee isn’t unreasonable.
Update: Michele now has an honest-to-goodness unscientific internet poll up on the subject.