The gunmen snatched the Emir of Gwoza, Alhaji Idriss Timta, and the Emir of Uba, Alhaji Ismaila Mamza, from vehicles on the road at Zhur, a remote community in the southern part of Borno state, as they were on their way to a funeral.
A government official said military had been deployed to the area in an attempt to rescue the hostages.
Boko Haram, which is fighting to reinstate an ancient Islamic caliphate in northern Nigeria, has been able to run riot across the north east - and bomb cities across the country - despite a year-long military offensive against the group.
Nigeria's president Goodluck Jonathan said on Thursday declared "total war" against Boko Haram, saying he had ordered a full-scale operation against the militants.
He sought to reassure parents of 219 schoolgirls who have been held by the group since last month that they would be freed.