Jefferson didn't say it

"Dissent is the highest form of patriotism."

It appears it was that patriotic American, Howard Zinn, who was the first one who used that exact phrase in 2002.

From the discussion at urbanlegends.about.com

an editorial in the Nov/Dec 2001 issue of The New Crisis, the NAACP magazine, here contains this sentence: “Thoughtful dissent, particularly when the blood is running hot, is one of the highest orders of patriotism."

The discussion also gives a longer, vaguely similar quote by TJ:

The man who loves his country on its own account, and not merely for its trappings of interest or power, can never be divorced from it, can never refuse to come forward when he finds that she is engaged in dangers which he has the means of warding off. —

TITLE: To Elbridge Gerry.
EDITION: Washington ed. iv, 188.
EDITION: Ford ed., vii, 151.
PLACE: Philadelphia ,
DATE: June. 1797