Maccagnan, 47, will be the Jets' third GM in the past four years, replacing John Idzik, who was fired after only two seasons.
Maccagnan represents the start of a new era for the Jets, who cleaned house after a 4-12 season.
"We interviewed a number of impressive, qualified candidates, but Mike Maccagnan clearly stood out," Jets owner Woody Johnson said. "Mike's attention to detail, strong personnel background and collaborative approach to evaluating players made it clear that he is the right choice to be the next general manager of the New York Jets."
Maccagnan was the only candidate invited back for a second interview, and he spent the past three days huddling with team officials at the Jets' facility in Florham Park, New Jersey. Unlike Idzik, who was forced to keep Rex Ryan in 2013, Maccagnan was set to have input into the selection of the next head coach, with the final call belonging to Johnson.
In hiring Maccagnan, the Jets have changed their power structure. He and Bowles will report directly to Johnson, who envisions the GM and coach as equal partners. Previously, the coach reported to the GM. Maccagnan will have control over the 53-man roster and final say on the draft; the coach will decide the weekly lineups. The lines were blurred with Ryan and Idzik, especially with quarterback decisions.
Clearly, Maccagnan's ties to Casserly played a huge role. Casserly and Ron Wolf, both former longtime GMs, were hired at the end of the season as consultants to advise Johnson throughout the concurrent searches for a GM and coach.
Casserly described Maccagnan as "an outstanding football man, one who is highly organized, and an excellent evaluator. He is very thorough in his preparation and will do a terrific job for the Jets."
Because of his connection to Maccagnan, Casserly took a background role during the first interview, allowing Wolf to lead the session.
Maccagnan impressed them with his cerebral, organized approach and his plan for improving the team, sources said. After the season, they reached out immediately to Maccagnan, who got his start in the NFL from Casserly, the former Washington Redskins and Texans GM.
Maccagnan was a Redskins' scout from 1995 to 2000, and he became one of Casserly's first hires with the Texans.
Maccagan is regarded in league circles as a grinder, a quiet and unassuming background player with solid evaluation skills. Some wonder if he'll be able to handle the glare of the New York spotlight.
He joined the Texans at their inception in 2000, rising to his most recent position in 2011. He was part of an organization that won two division titles (2011-2012). The Texans drafted well from 2009 to 2011, the year they picked defensive star J.J. Watt, but their last three drafts have produced no Pro Bowl players and only a handful of starters.
The Jets interviewed at least six other candidates for the job, all of whom are front-office executives -- Rod Graves (Jets), Chris Grier (Miami Dolphins), Trent Kirchner (Seahawks), Bill Kuharich (Cleveland Browns), Rick Mueller (Philadelphia Eagles) and Jon Robinson (Tampa Bay Buccaneers). They were spurned by four others -- Chris Ballard (Kansas City Chiefs), Eric DeCosta (Baltimore Ravens), George Paton (Minnesota Vikings) and Ryan Pace (New Orleans Saints), who was hired by the Chicago Bears.
The Jets have gone four straight years without making the playoffs, failing to post a winning record in any of those seasons. Mike Tannenbaum was fired after a 6-10 mark in 2012, replaced by Idzik, who went 12-20.
Unlike Idzik, who walked into a bad salary-cap situation, Maccagnan will have the flexibility to make immediate improvements. The Jets have more than $40 million in salary-cap space and they own the sixth pick in the draft.
On the downside, the team has a big question at quarterback and only one Pro Bowl player on the roster -- center Nick Mangold.
Maccagnan will have plenty of big decisions in the coming months.
From a personnel standpoint, he has to evaluate inconsistent quarterback Geno Smith, decide whether wide receiver Percy Harvin is worth his $10.5 million salary for 2015 and determine how much to spend on free-agent linebacker David Harris.
"[The Jets have] a solid foundation of players." Maccagnan said. "As with all teams, there are some areas we need to address, but we're going to hire the right head coach, evaluate our personnel and work together to build a football operation to get the New York Jets back on the winning track."