Thomas played all 16 games (10 started) in 2003 with a sack, 3 passes defended, one fumble recovery, and 26 total tackles.

Thomas played in 14 games (6 started) of the 2004 season with 1.5 sacks, a pass defended, and 28 total tackles.

In particular, comments made by Thomas during the 2007 season where he said he had not thought it necessary to "continue to work to improve" left many Jets fans extremely concerned.

Overall, Thomas finished the 2007 season with 2.5 sacks, one pass defended, a forced fumble, and 39 total tackles.

Thomas had a mediocre 2008 season as he collected 5.5 sacks, one pass defended, 2 forced fumbles (1 recovery), and 38 total tackles.

He led the Jets to the playoffs for the second season in a row but lost the AFC Championship to the Pittsburgh Steelers.