The attack on Kukuwa in Yobe state happened last Thursday but details have only just emerged from survivors.
Some of the villagers are said to have drowned while fleeing gunmen.
The BBC's Nigeria reporter says the fact it took five days for any news to come out shows how dire the security situation is in parts of Yobe state.
A military spokesman said that following air surveillance and armed reconnaissance, the reports of a massacre and drownings could not be substantiated.
However, eyewitnesses said that dozens of militants arrived in the village on motorcycles and began shooting the residents.
"We were getting ready to observe evening prayers, all of a sudden we started hearing sounds of gunshots," one man told the BBC Hausa service.
"We all ran for our dear life into the bush. The following morning we returned home and discovered corpses of 60 children. They all drowned in the river in their effort to escape the attack."
Some accounts put the death toll higher than 60 but exactly how many people died remains unclear.
A regional military offensive has weakened the Islamist group in recent months but parts of north-east Nigeria, such as Yobe and neighbouring Borno state, 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.
He has ordered the military to defeat Boko Haram within three months.