In a 2000 American Perspective Article, Where Have You Gone, Franklin Roosevelt?, Michael Nelson says:
In 1948 Professor Arthur M. Schlesinger, Sr. called on 55 of his fellow historians to grade each president (excluding the incumbent, Harry S. Truman) as either "great," "near great," "average," "below average," or a "failure." When Schlesinger averaged each president's grades, Abraham Lincoln, George Washington, Franklin D. Roosevelt, Thomas Jefferson, Woodrow Wilson, and Andrew Jackson scored as great presidents, Ulysses S. Grant and Warren G. Harding were rated as failures, and the rest fell in between.

In his second survey in 1962, Truman ended up in ninth place as a near-great president in the company of John Adams and Theodore Roosevelt. Dwight D. Eisenhower ranked 22nd. Republicans howled that Schlesinger had packed the jury with Democrats.

His son, commissioned a study in 1996. Eisenhower's stock has risen since the 1960s (he now regularly shows up among the top 10) but less because of any new appreciation of what long was thought to be his passive style of leadership than because of recent archival research that shows him to have been a deceptively strong "hidden-hand" leader.

Rankings are based on averages of 6 quantitative rankings by groups of scholars from 1996 to 2005 as listed at Historical rankings at WikipediA, with the scores summarized in a 10 pt. rating (10 - Great, 1-Failure). *

No.	Name	Pty	State	Dates	Rat- ing	Previous
1	Washington, George	F	VA	1789-97	10	General
2	Adams, John	F	MA	1797-1801	7	VP - Founding Father from MA
3	Jefferson, Thomas	D-R	VA	1801-09	9	Founding Father from VA
4	Madison, James	D-R	VA	1809-17	7	Founding Father - Representative from VA - "Father of the Constitution"
5	Monroe, James	D-R	VA	1817-25	7	VA Senator
6	Adams, John Quincy	R/W	MA	1825-29	6	MA Monroe's Secy of State
7	Jackson, Andrew	D	TN	1829-37	8	TN War of 1812 General
8	Van Buren, Martin	D	NY	1837-41	4	In Jackson's cabinet
9	Harrison, William Henry	W	IN	1841-	2	Governor of IN
10	Tyler, John	W	VA	1841-45	2	VP
11	Polk, James	D	TN	1845-49	8	Congressman from TN
12	Taylor, Zachary	W	MS	1849-50	3	Mexican War General
13	Fillmore, Millard	W	NY	1850-53	2	VP - Succeeded
14	Pierce, Franklin	D	NH	1853-57	1	NH Senator
15	Buchanan, James	D	PA	1857-61	1	PA Senator and Polk's Secretary of State
16	Lincoln, Abraham	R	IL	1861-65	10	IL Congressman
17	Johnson, Andrew	D	IN	1865-69	1	TN Senator, VP succeeded
18	Grant, Ulysses S.	R	OH	1869-77	2	Civil War Union General
19	Hayes, Rutherford B.	R	OH	1877-81	4
20	Garfield, James	R	OH	1881-81	3	Ohio Senator
21	Arthur, Chester	R	NY	1881-85	4	VP - Succeeded
22, 24	Cleveland, Grover	D	NY	1885-89, 1893-97	6	NY Governor
23	Harrison, Benjamin	R	IN	1889-93	3	Senator from Indiana
25	McKinley, William	R	OH	1897-1901	6	Congressman, OH Governor
26	Roosevelt, Theodore	R	NY	1901-09	9	NY Governor - VP Succeeded
27	Taft, William H.	R	OH	1909-13	5	Roosevelt's Secretary of War
28	Wilson, Woodrow	D	NJ	1913-21	8	NJ Governor
29	Harding, Warren	R	OH	1921-23	1	Governor of Ohio
30	Coolidge, Calvin	R	MA	1923-29	4	MA Governor
31	Hoover, Herbert	R	IA	1929-33	3	Coolidge's Secretary of Commerce
32	Roosevelt, Franklin D.	D	NY	1933-45	10	Governor of NY
33	Truman, Harry S	D	MO	1945-53	8	Senator from MO, VP Succeeded
34	Eisenhower, Dwight	R	TX/ NY	1953-61	8	General - President of Columbia U.
35	Kennedy, John F.	D	MA	1961-63	7	MA Senator
36	Johnson, Lyndon	D	TX	1963-69	7	TX Senator, VP Succeeded
37	Nixon, Richard	R	CA	1969-74	4	CA Senator, VP
38	Ford, Gerald	R	MI	1974-77	4	MI Congressman, VP Succeeded
39	Carter, Jimmy	D	GA	1977-81	4	GA Governor
40	Reagan, Ronald	R	CA	1981-89	7	CA Governor
41	Bush, George H.W.	R	TX	1989-93	5	VP
42	Clinton, William J.	D	AR	1993-2001	5	AR Governor
43	Bush, George W. †	R	TX	2001-08	2	TX Governor
43	Obama, Barack	D	IL	2009-		IL Senator

Average: Republicans - 4.7, Democrats - 5.3

* To compute the 10 pt. rating I basically did a linear distribution of averages of the 6 most recent rankings, placing breaking points (e.g. between 9 and 10) where there were gaps in the averages. It might have been better to use a bell curve, since you would expect more average (5 & 6) presidents than extremely good or bad ones (10's or 1's). Actually the natural breaks came up with only three 10's and three 9's, where a true linear distribution would have had 4 of each.

† George W. Bush's would have been a 5, based on a 2002 poll from Siena Research Institute (SRI) and a Federalist Society poll in 2005 published in the Wall Street Journal, since then his public approval rating (see below) has dropped because of the Iraq war and economic crisis.
By the end of 2008 his approval rating was down to 20-27%
See American Research Group and Gallup polls.
According to CNN he is "the most unpopular president in modern American history."
The TimesOnline ranked him 37 out of 42 in October 2008.

Pty - Party: F- Federalist, D-R - Democratic-Republican, R-W National Republican/Whig, W - Whig R - Republican, D - Democrat

The top ten based on individual ranks from 1-43 are:

Rank	President	Range
1	Abraham Lincoln	1-  3
2	Franklin D. Roosevelt	1-  3
3	George Washington	1-  4
4	Theodore Roosevelt	3-  5
5	Thomas Jefferson	2-  7
6	Harry S. Truman	5-  8
7	Woodrow Wilson	6-11
8	Andrew Jackson	6-13
9	Dwight D. Eisenhower	8-12
10	James K. Polk	9-14
	John Adams	9-16
	John Kennedy	8-18

The Times Online includes Ronald Regan (8) instead of Andrew Jackson.

Nelson says "Although Greenstein claims to have "avoided presidential rankings,". Surely the historians were right to place Kennedy, Johnson, and Truman above Nixon and Ford, in contrast to Greenstein's arrangement. But they were wrong to rank Reagan with the average presidents (as they did in Schlesinger, Jr.'s 1996 survey), just as Greenstein is right to rate him more highly."

The greatness of the presidents in Landy and Milkis's ("Presidential Greatness") hall of fame--Washington, Jefferson, Jackson, Lincoln, and FDR--has less to do with power than with purpose. Great presidents are "conservative revolutionaries" who in uncertain times "teach the nation about the need for great change but also about how to reconcile change with American constitutional traditions and purposes.

See: George W. Bush Approval Ratings at Gallup
and a summary of other rankings at the Roper Center

Links:
Where Have You Gone, Franklin Roosevelt? by Michael Nelson for the American Perspective Nov., 2000
Historical rankings of United States Presidents at WikipediA
Historical rankings of United States Presidents at Answers.com
Gallup Public Poll
What Makes a President Great?, 2005 poll for the Federalist Society by James Lindgren, published in the Wall Street Journal

Books:

• The Presidential Difference, 2000, by Fred I. Greenstein at Princeton U., 2000
• Presidential Greatness, 2000, by Marc Landy of Boston College and Sidney M. Milkis of the University of Virginia.