What three Middle Colonies offered religious freedom?
While it depends a bit on how you're defining the "middle," Pennsylvania, New York, and New Jersey were religiously diverse.
Start with Pennsylvania: founded by William Penn, he saw his charter as an opportunity for a "Holy Experiment." Penn's Quaker beliefs supported equal treatment for many, making Pennsylvania (and, by extension, Delaware, as Delaware was part of the original charter until it broke off officially on the eve of the Revolution) one of the most religiously diverse colonies.
New York and New Jersey were also relatively religiously diverse -- less because of particular policies, and more because a number of other European nations were well represented in these colonies. The Dutch had claims along the Hudson River before the English arrived, as did the Swedes. The founding of these colonies, unlike New England's, which were largely driven by folks seeking religious refuge, was driven more by opportunities for work.