The three named as by the State Department were Abubakar Shekau, Abubakar Adam Kambar and Khalid al-Barnawi.
"In the last 18 months, Boko Haram or associated militants have killed more than 1,000 people," the State Department said in a statement, adding that Shekau was the most visible of the group's leaders.
However, the US stopped short of putting the group as a whole on its terror list.
"These designations demonstrate the United States' resolve in diminishing the capacity of Boko Haram to execute violent attacks," the statement said.
Boko Haram has been waging war to install an Islamic government and Sharia rule in Nigeria, Africa's largest oil producer.
The two other men were accused of close ties to al-Qaeda in the Islamic Maghreb, which has been designated as a foreign terrorist organisation by the United States.
"Under Shekau's leadership, Boko Haram has claimed responsibility for numerous attacks in northern Nigeria, its primary area of operation," the statement said.
The US move blocks the three men's "property interests subject to US jurisdiction and prohibits US persons from engaging in transactions with or for the benefit of these individuals," the statement added.
Boko Haram is credited with the August 26, 2011 attack on the United Nations building Abuja that killed at least 23 people and injured scores of others.
Boko Haram's deadliest violence occurred on January 20, 2012 in Kano, Nigeria, with a series of attacks that killed more than 180 people.
The group has also claimed responsibility for a series of suicide attacks on churches in Kaduna state last Sunday that left at least 16 people dead. They also sparked reprisals by Christian mobs against mosques and Muslims that killed nearly 100 people.
