The insurgents, disguised in military uniforms, burned scores of homes and buildings during the onslaught late Tuesday.
Saidu Yakuba of the Environmental Protection Agency in Borno state said Thursday 87 bodies had been recovered so far and officials were still searching for more dead. Another officer of the agency said 143 bodies had been recovered.
Officials said Boko Haram militants set up checkpoints and gunned down civilians trying to flee to safety.
The group says it is fighting to impose a strict form of Islamic law on Nigeria's Muslim-majority north. The group has been blamed for thousands of deaths since launching an uprising against the government in 2009.
Borno is one of three northeastern states where President Goodluck Jonathan declared a state of emergency and deployed additional troops in May to fight Boko Haram. Rights groups have criticized the military for heavy-handed operations they say have led to hundreds more deaths.