San Diego Unified Schools' Supt. Thomas W. Payzant has accepted an extension of his contract this week that will raise his salary to $100,000 in 1987-88. After nearly three years of various administrative and educational reforms instigated by the 44-year-old superintendent, school board members voted unanimously to offer Payzant a contract that would raise his current annual salary of $85,000 to $90,000 on Nov. 1, then to $95,000 on Nov. 1, 1986, and to $100,000 on Nov. 1, 1987. "I'm very pleased with their decision," Payzant said. "I've got a lot more to do in San Diego schools."