The Lake Chad area - a vast maze of tiny islands and swampland sheltering thousands of Nigerian refugees - is thought to be serving as a hideout for the Islamist insurgent group.
"There was heavy weapons and machine gun fire from about 2000 local time," said a resident of Niger's nearby lakeside town of N'Guigmi, which Boko Haram attempted to seize earlier this month. Two security forces also confirmed the attack, without providing further details.
It was not immediately clear which island had been attacked on Friday and whether it was inhabited, but the security sources and residents said it was in Niger and within 50 km (30 miles) of the borders with Chad and Nigeria.
One of the security sources said it would provide a strategic, concealed base for the militants to co-ordinate future attacks if they won control.
Last week, Boko Haram fighters aboard motorized canoes attacked a lakeside fishing village in Chad, killing at least five people in the group's first known lethal attack on that country.
The Sunni group, which has killed thousands of people in a six-year insurgency in Nigeria, has been gaining strength in the past year. It has carved out a territory the size of Belgium in the northeast of the country and intensified cross-border raids.
But regional forces from Nigeria, Chad, Cameroon and Niger have won battles against the group in recent weeks as they seek to hem them within their heartland.