Request for Question Clarification :

I spent long searching hours but I could not find the information to compile the list you requested.
The closest thing I found is a pubblication I could point you to that claims contains the latest, most comprehensive financial and operational data from America's museums. It claims contains numbers on attendance, operating and non-operating income and expenses, earned income sources, and costs of collections care etc. Data are coming from a survey of 800 museums of all types

Clarification of Question :

sorry for the late reply but since you did the work then please do go
ahead and send the answer.

Answer :

you can purchase the publication I mentioned from the American
Association of Museums, the link for the purchase is below

http://www.aam-us.org/bookstore/detail.cfm?id=495

This is the list I compiled. As I said the list is only ranked by attendance

Washington DC National Gallery of Art: 6.000,000
New York, NY Metropolitan Museum of Art: 5,500,000
New York, NY MoMA: The Museum of Modern Art: 1,500,000
Chicago, IL The Art Institute of Chicago: 1,478,000
Houston, TX The Museum of Fine Arts, Houston: 1,100,000
New York, NY Guggenheim Museum Annual: 925,000
Pittsburg, PA Carnegie Museum of Art Annual: 860,000
Alexandra, VA Torpedo Factory Art Center, Alexandria, VA: 800,000
Los Angeles, CA LACMA: Los Angeles County Museum of Art: 800,000
Philadelphia, PA Philadelphia Museum of Art: 800,000
Washington DC Hirshhorn Museum and Sculpture Garden: 784,000
San Francisco, CA California Palace of Legion of Honor: 750,000
Cleveland, OH Cleveland Museum of Art: 630,000
San Francisco, CA San Francisco Museum of Modern Art: 600,000
Detroit, MI The Detroit Institute of Arts Annual: 591,000
Washington DC Freer Gallery of Art and Arthur M. Sackler Gallery: 583,000
San Marino,CA Huntington Library, Art Collections: 565,000
Brooklyn, NY Brooklyn Museum of Art: 500,000
Phoenix, AR Phoenix Art Museum: 500,000
Minneapolis, Minnesota The Minneapolis Institute of Arts: 500,000
St. Louis, MO Saint Louis Art Museum: 480,000
Los Angeles, CA The Getty: 400,000
Dallas, TX Dallas Museum of Art: 400,000
San Diego, CA San Diego Museum of Art SDMA: 400,000
Washington DC National Museum of American Art: 400,000
Seattle, WA Seattle Art Museum: 400,000
Scottsdale, AR Scottsdale Museum of Contemporary Arts: 380,000
Richmond, VA Virginia Museum of Fine Arts VMFA: 368,000
Washington DC National Portrait Gallery: 350,000
Los Angeles, CA MOCA: Museum of Contemporary Art: 350,000
Portland, OR Portland Art Museum: 350,000
New Orleans, LA New Orleans Museum of Art: 344,000
Denver, CO Denver Art Museum: 334,000
Atlanta, GA High Museum of Art: 310,000
Fort worth, TX Kimbell Art Museum: 284,000
Washington DC National Museum of African Art : 281,000
Sarasota, FL Ringling Museum of Art: 280,000
Baltimore, MD The Baltimore Museum of Art: 278,000
New York, NY Whitney Museum of American Art: 274,000
New York, NY Frick Collection: 270,000
Berkeley, CA Berkeley Art Museum and PFA: 260,000
Washington DC Corcoran Gallery of Art: 250,000
Oakland, CA Oakland Museum of California: 250,000
St. Petersburg, FL Salvador Dali Museum: 250,000
Cody, WY Whitney Gallery of Western Art: 250,000
New York, NY The Jewish Museum : 225,000
Stockbridge, MA Norman Rockwell Museum: 225,000
San Francisco, CA San Jose Museum of Art: 200,000
Laguna Beach, CA Laguna Art Museum: 200,000
Washington DC The Phillips Collection: 200,000
Boston, MA Isabella Stewart Gardner Museum: 172,000
Hartford, CT Wadsworth Atheneum: 160,000
San Francisco, CA Yerba Buena Center for the Arts: 150,000
Sacramento, CA Crocker Art Museum ; 150,000
Pasadena Norton Simon Museum: 150,000
La Jolla, CA Museum of Contemporary Art San Diego: 135,000
Worcester, MA Worcester Art Museum: 135,000
Santa Barbara, CA Santa Barbara Museum of Art: 130,000
Los Angeles, CA UCLA Armand Hammer Museum: 120,000
Seattle, WA Frye Art Museum: 102,000
Tacoma, WA Tacoma Art Museum: 100,000
New York, NY The Drawing Center: 100,000
San Diego, CA Timken Museum of Art: 93,000
Reno, NV Nevada Museum of Art NMA: 90,000
Pennsylvania Doylestown, PA James A. Michener Art Museum: 90,000
Chicago, IL Museum of Contemporary Art: 80,000
The Modern Art Museum of Ft. Worth: 80,000
Philadelphia, PA The Pennsylvania Academy of Fine Arts: 75,000
The Pennsylvania Academy of Fine Arts: 75,000
Newport Beach, CA Orange County Museum of Art: 70,000
Pittsburg, PA Andy Warhol Museum: 70,000
Seattle, WA Henry Art Gallery Seattle: 65,000
Las Vegas, NV Las Vegas Art Museum: 59,000
Philadelphia, PA Rodin Museum: 58,000
Davis, CA John Natsoulas Gallery: 50,000
Bennington, VT Bennington Museum, Vermont: 50,000
Santa Fe, NM Georgia O'Keeffe Museum: 30,000
Irvine, CA Irvine Museum: 16,000
Davis, CA UC Davis Galleries & Museums: 13,400
Poplar Bluff, MO Margaret Harwell Art Museum: 13,000