There were certainly Congregational Puritans, but Presbyterianism was the primary Puritan ecclesiology. This is evidenced from the Westminster Standards, notably the Form of Presbyterian Church Government. London and Edinburgh were the centers of Presbyterianism; congregationalism was centered more in New England.

Jonathan Edwards - Presbyterian
http://www.puritanboard.com/f47/john...siology-16318/
Congregational vs. Presbyterian

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Andrew Myers
Husband of Jessica, Father of Jackson, Katie and Samuel
Member, Presbyterian Reformed Church of Northern Virginia
Warrenton, VA USA
Editor, The Matthew Poole Project

"Let your Morning Thoughts, and your last Evening Thoughts, be what shall become of you to all Eternity." -- Matthew Poole