Yankees general manager Brian Cashman said this week that because of the large numbers involved, it was "pretty obvious" to him that the team would be turning down those options.
Berkman, 34, was acquired from the Astros on July 31 with the understanding that his $15 million club option for next season would not be picked up, with a $2 million buyout in place instead.
Berkman hit .255 with one home run and nine RBIs in 37 regular-season games for New York and said that he would prefer to play for a team where he could play first base more regularly. With Mark Teixeira in place, Berkman's duty was largely confined to the designated-hitter role.
Johnson, 32, was limited to just 24 games due to injury after signing as a free agent, batting .167 with two home runs and eight RBIs. He had a mutual option for 2011 worth $5.5 million and instead receives a $250,000 buyout.
Wood, 33, was 2-0 with a 0.69 ERA in 24 regular-season relief appearances for New York after coming over in a July 31 trade from the Indians, posting the lowest single-season ERA in franchise history (minimum 25 innings). Wood's mark eclipsed Goose Gossage's 0.71 ERA from 1981.
The right-hander's 2011 option was for $11 million, a high price for the Yankees to pay Mariano Rivera's setup man. It is possible the Yankees could attempt to re-sign Wood, though it is likely he will also field offers from teams in need of a closer.
The Yankees did choose to exercise the 2011 option on the contract of right-hander Andrew Brackman, whose original four-year, $4.55 million deal ran through the end of this season.
Brackman turns 25 in December and has yet to make his Major League debut, though he was on the active roster in September. New York holds club options on Brackman through 2013.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.