“Boisterous sea of liberty” and “tempestuous sea of liberty” both are from letters by Thomas Jefferson (1743-1826). In an April 24, 1796 letter to Philip Mazzei (1730-1816), Jefferson wrote:
 
“Against us are the Executive, the Judiciary, two out of three branches of the legislature, all of the officers of the government, all who want to be officers, all timid men who prefer the calm of despotism to the boisterous sea of liberty, ...”
 
In May 1797, however, the New York Minerva printed “all timid men who prefer the calm of despotism to the tempestuous sea of liberty.” This was reprinted in many newspapers and “tempestuous sea of liberty” (not “boisterous”) became popularly known in the early 1800s.
 
“Boisterous sea of liberty” was used in two Jefferson letters in 1820 and replaced “tempestuous sea of liberty” in popular literature by the end of the 1800s. Jefferson wrote in an October 20, 1820 letter to Richard Rush (1780-1859):
 
“The boisterous sea of liberty is never without a wave.”
 
Jefferson repeated this phrase in a December 26, 1820 letter to Gilbert du Motier, Marquis de Lafayette (1757-1834):
 
“The boisterous sea of liberty indeed is never without a wave, and that from Missouri is now rolling towards us, but we shall ride over it as we have over all others.”
 
     
The Papers of Thomas Jefferson (Princeton University)
Thomas Jefferson to Philip Mazzei
Monticello Apr. 24. 1796.
(...)
The aspect of our politics has wonderfully changed since you left us. In place of that noble love of liberty and republican government which carried us triumphantly thro’ the war, an Anglican, monarchical and aristocratical party has sprung up, whose avowed object is to draw over us the substance as they have already done the forms of the British government. The main body of our citizens however remain true to their republican principles, the whole landed interest is with them, and so is a great mass of talents. Against us are the Executive, the Judiciary, two out of three branches of the legislature, all of the officers of the government, all who want to be officers, all timid men who prefer the calm of despotism to the boisterous sea of liberty, British merchants and Americans trading on British capitals, speculators and holders in the banks and public funds a contrivance invented for the purposes of corruption and for assimilating us in all things, to the rotten as well as the sound parts of the British model.
     
The Papers of Thomas Jefferson (Princeton University)
Extract and Commentary Printed in the New York Minerva
[2 May 1797]
“Our political situation is prodigiously changed since you left us. Instead of that noble love of liberty, and that republican government, which carried us triumphantly thro’ the dangers of the war, an Anglo—Monarchico—Aristocratic party has arisen.—Their avowed object is to impose on us the substance, as they have already given us the form, of the British government. Nevertheless, the principal body of our citizens remain faithful to republican principles. We have against us (republicans) the executive power, the judiciary power, (two of the three branches of our government) all the officers of government, all who are seeking offices, all timid men who prefer the calm of despotism to the tempestuous sea of liberty, the British merchants and the Americans who trade on British capitals, the speculators, persons interested in the banks and the public funds.”
 
6 May 1797, Federal Gazette & Baltimore Daily Advertiser (Baltimore, MD), pg. 2, col. 3:
TRANSLATED FOR THE MINERVA.
From the Paris Monitor, of January 25.
FLORENCE, January 1.
LETTER
From Mr. Jefferson, late Minister of the United States in France, and Secretary to the Department of Foreign Affairs, to a citizen of Virginia.
This letter, literally translated, is addressed to M. Mazzei, author of Researches, historical and political, upon the United States of America, now resident in Tuscany.
 
“Our political situation is prodigiously changed since you left us. Instead of that noble love of liberty, and that republican government, which carried us triumphantly thro’ the dangers of the war, an Anglo—Monarchico—Aristocratic party has arisen.—Their avowed object is to impose on us the substance, as they have already given us the form, of the British government. Nevertheless, the principal body of our citizens remain faithful to republican principles. We have against us (republicans) the executive power, the judiciary power, (two of the three branches of our government) all the officers of government, all who are seeking offices, all timid men who prefer the calm of despotism to the tempestuous sea of liberty, the British merchants and the Americans who trade on British capitals, the speculators, persons interested in the banks and the public funds.”
 
20 August 1798, Springer’s Weekly Oracle (New London, CT), pg. 1, col. 3:
This was the state, which this party, so obnoxious to Mr. Jefferson, preferred “TO THE TEMPESTUOUS SEA OF LIBERTY”—a sea, whose waves are waves of blood—whose storms are the conflicting passions of Man—whose inhabitants are ferocious monsters, roaming their sanguinary round for prey—and whose shores are white with the bones of murdered millions.
(From an oration by Theodore Dwight—ed.)
 
1 October 1816, Weekly Aurora (Philadelphia, PA), pg. 273, col. 1:
THE TEMPESTUOUS SEA OF LIBERTY.
(Col. 3—ed.)
Then comes the tug of contention—the tempestuous sea of liberty—the good and evil passions of nature enter into conflict. Free government is maintained if the people are virtuous and true to themselves.
 
If the people become depraved, there is an end of free government—they verify the adage of the disciples of iniquity, they become their own worst enemies.
 
Monticello.org
Quotations on Liberty
(...)
1820 Oct. 20. (to Richard Rush) “The boisterous sea of liberty is never without a wave.”
 
The Jefferson Cyclopedia
4715. LIBERTY, Sea of.—
The boisterous sea of liberty is never without a wave.—
TITLE: To Richard Rush.
EDITION: Washington ed. vii, 182.
PLACE: Monticello
DATE: 1820
 
Academic Museum
Thomas Jefferson to Lafayette, Monticello, December 26, 1820
With us things are going on well.  The boisterous sea of liberty indeed is never without a wave, and that from Missouri is now rolling towards us, but we shall ride over it as we have over all others.
 
Google Books
The Columbia Book of Quotations
By Robert Andrews
New York, NY: Columbia University Press
1993
Pg. 517:
The boisterous sea of liberty is never without a wave.
THOMAS JEFFERSON (1743-1826), U.S. president. Letter, 20 Oct. 1820.
 
OCLC WorldCat record
The boisterous sea of liberty : a documentary history of America from discovery through the Civil War
Author: David Brion Davis; Steven Mintz
Publisher: New York : Oxford University Press, 1998.
Edition/Format:   Book : English
Summary:
Drawing on a gold mine of primary documents - including letters, diary entries, personal narratives, political speeches, broadsides, trial transcripts, and contemporary newspaper articles - The Boisterous Sea of Liberty brings the past to life in a way few histories ever do. Here is a panoramic look at American history from the voyages of Columbus through the bloody Civil War, as captured in the words of Benjamin Franklin, Thomas Jefferson, George Washington, Andrew Jackson, Abraham Lincoln, Frederick Douglass, Harriet Beecher Stowe and many other historical figures, both famous and obscure. In these pieces, the living voices of the past speak to us from opposing viewpoints - from the vantage point of loyalists as well as patriots, slaves as well as masters - providing a more sophisticated understanding of the forces that have shaped our society, from the power of public opinion to the nearly absolute power of the slaveholder. The Boisterous Sea of Liberty is a documentary history of America, which uses the first-person testimony to reconstruct the basic forces, events, ideas, and struggles that shaped American society during its formative era. It places the defining documents of American history in their proper context and presents a lively and innovative interpretation of our history from earliest colonization through the Civil War.
 
Google Books
The Yale Book of Quotations
Edited by Fred R. Shapiro
New Haven, CT: Yale University Press
2006
Pg. 395:
Thomas Jefferson
U.S. president, 1743-1826
“The boisterous sea of liberty is never without a wave.”
Letter to Marquis de Lafayette, 26 Dec, 1820. Jefferson had earlier used boisterous sea of liberty in a letter to Philip Mazzei, 24 Apr. 1796.