The attack on Kukuwa in Yobe state happened last Thursday but details have only just emerged from survivors.
Some of the villagers who died are said to have drowned while fleeing gunmen.
The BBC's Nigeria correspondent says the fact that it took five days for any news to come out demonstrates how dire the security situation is in Yobe.
Eyewitnesses told AFP news agency that dozens of militants arrived in the village on motorcycles and began shooting the residents.
"They opened fire instantly, which forced residents to flee. Unfortunately many residents who tried to flee plunged into the river which is full from the rain. Many drowned," Modu Balumi, a resident, told AFP.
Some accounts put the death toll higher than 60 but exactly how many people died remains unclear.
A military offensive has weakened the extremist group in recent months but parts of north-east Nigeria are still extremely insecure.
Kukuwa is about 50km (30 miles) from the state capital Damaturu but the people there have for some time been extremely vulnerable.
Last month, Boko Haram killed 10 people there after some of its own fighters had been killed by a vigilante force in the village.
The southern part of Yobe has witnessed some of the most shocking attacks launched by Boko Haram fighters in recent years.
In February last year, militants targeted a boarding school in Buni Yadi killing 59 boys in their dormitories. In 2013, dozens of students were killed at an agricultural college in the same area.
The BBC's Will Ross in Lagos says that in general, the security situation has improved in Nigeria since then - but the challenge is still immense.
Close to 1,000 people have been killed by Boko Haram since President Muhammadu Buhari took over in May.
Reports in Nigeria say as many as 60 people may have been killed after a raid on a village in the north-east by suspected Boko Haram militants.