William J. McCarthy, the Teamsters' top man in New England for two decades, Friday upset Jackie Presser's hand-picked choice to succeed him as president of the nation's largest union. The Teamsters' 17-member General Executive Board picked McCarthy, 69, of Boston over Secretary-Treasurer Weldon Mathis, who Presser had named acting president on May 4. While several of the Teamsters' 16 regional vice presidents had jockeyed for position to succeed Presser, the race had narrowed to McCarthy and Mathis last week. McCarthy, who has a reputation of being a tough negotiator with a quick temper, will serve out Presser's five-year term, which expires in 1991.