The Jackals were chosen to host the 2000 Northern League All-Star Game at Yogi Berra Stadium. However, it was one of few highlights in an otherwise down year. New Jersey failed to finish with a winning record for the first time in team history and finished up the season at 31–52. Manager Kash Beauchamp resigned at the end of the season and the team chose Waterbury Spirit manager George Tsamis to replace him.
In Tsamis' first season the Jackals again struggled. The team finished five games under .500 in the first half of the season, but was able to even their record by finishing five games above .500 in the second half. Their 45–45 record barely qualified the Jackals for the 2001 Northern League playoffs, but the team managed to sweep Albany-Colonie in the first round. They then took on the Elmira Pioneers in the Northern League East Championship Series, winning in five games. The Jackals completed their run by defeating the North Division champion, the Winnipeg Goldeyes, 3 to 1 to claim their first Northern League Championship.
The 2002 Jackals season was historic on two fronts. The first historic moment came when Jeremy Callier threw a no-hitter on August 28 against the Berkshire Black Bears, requiring a home run by Ryan Kane in the bottom of the ninth inning to make it official. The second piece of team history saw the Jackals set a team record for victories, finishing with 62 to lead the league. In the playoffs, however, the Jackals did not have any relative ease in winning games as they were taken to five games by Elmira again in the first round and required a two-out bases clearing double by first baseman Dave Callahan to win over the Adirondack Lumberjacks in the fifth game of their Northern League East Championship Series tilt. Once again, though, the Jackals finished with a championship by defeating Winnipeg in four games.
2003 saw two major changes for the Jackals. After Tsamis resigned following the year to take the managerial position with the St. Paul Saints, New Jersey hired Gary SouthShore RailCats manager Joe Calfapietra to take his place. The second saw the end of the merger with the Northern League, as the Northeast League once again became its own entity. The Jackals returned to the playoffs for a third consecutive year by winning both halves of the season in their division, but were dispatched in the first round by the eventual league champion Brockton Rox. Despite this, the Jackals finished with a 52–37 record.
In 2004, New Jersey improved their record to what was then the team's second-best showing in its history, winning 54 games and losing 29. However, the first half of the season required saw the Jackals end in a tie with the New Haven County Cutters, requiring a one-game playoff which New Jersey won for their fifth consecutive half-season victory. The Jackals pulled away in the second half with a 28–18 record, winning both halves for a third straight year. After dispatching of the Bangor Lumberjacks in the first round of the playoffs, the Jackals found themselves in trouble against the North Shore Spirit in the league championship series. Trailing two games to none and down late in the third game, the Jackals rallied for an extra inning victory. They duplicated the feat the next day in Game 4 to tie the series, and then won the fifth and deciding game to take the Northeast League Championship. To date, this is the last time the Jackals have won a league championship.
In 2005 the Jackals joined the Can-Am League and failed to make the playoffs for the first time since 2000 despite posting a winning record of 48–44. 2006 saw another history-making performance as Aaron Myers threw the second no-hitter in team history, but New Jersey again missed the playoffs and- with a 43–48 record- finished with only their second losing record in team history.
The Jackals won the Can-Am League First Half Championship in 2007 with a 31–15 record, guaranteeing them a spot in the playoffs. Their 31 wins in the first half still mark a franchise best in the first half, and second most in a half (32 in 2002). The Jackals' second half was not as strong, as they finished in last place with an 18–29 record. New Jersey took the Nashua Pride to a fifth game at Yogi Berra Stadium in their best-of-five series before losing and getting knocked out. The Jackals missed the playoffs in 2008, finishing 43–51.
New Jersey was able to ride a CanAm League record 14 game win streak to a First Half Championship in 2009 with a 28–19 record, once again guaranteeing the team a playoff spot. The Jackals won 27 games in the second half for a total of 55, the second most in team history. Despite that, New Jersey was quickly eliminated from the playoffs by the Worcester Tornadoes.
For the second time in their history, the Jackals lost 50 games in 2010. However, their combined record of 42–50 was enough for the team to qualify as one of four teams in what was now a seven-team Can-Am League. For the second consecutive year, though, the Jackals were swept in the first round of the playoffs; this time, the defending league champion Quebec Capitales defeated the Jackals.