In the American colonies, which document called for religious freedom?

No single document called for religious freedom across all of the colonies because religious freedom was not supported by all of the colonies. The New England colonies of Connecticut and Massachusetts (including modern day Maine) were founded by Puritans. Religious intolerance was prevalent, and dissenters or proselytizers could be harshly punished or exiled. After England passed the Toleration Act, some of these punishments abated, though discrimination was still prevalent.
In the Southern and Middle Colonies there was more religious diversity and a bit more tolerance, though a number of the colonies retained official religions and required tithing to that religion. Eight of the thirteen colonies had officially established religions.
Three states were notable for their religious freedom. Rhode Island was founded by Roger Williams after he escaped from punishment in Massachusetts. His opinions about not stealing land from Native Americans made him unpopular, and he was almost returned to England. Instead, he founded Rhode Island and wrote his view on religious freedom into its founding documents.
Maryland was founded by Catholics and initially viewed Catholicism as the only acceptable religion. However, the prosperity of the colony brought many Protestants, leading the Catholic founders to pass a Tolerance Act for all Christian religions in order to prevent discrimination against Catholics. Non-Christians were still unwelcome in Maryland at this point.
Pennsylvania was founded by Quakers and recognized religious freedom because of the discrimination that Quakers had faced previously. Religious freedom was written into their founding charter.