From the Office of the Controller, here are the biggest ones I found.
download current controller report (PDF)
The Top five non profits are
CALIFORNIA ACADEMY OF
SCIENCES
x PROFESSIONAL &
SPECIALIZED SERVICES
DEPARTMENT OF PUBLIC
WORKS
$66,974,017 $18,280,466 $2,767,359
TENDERLOIN HOUSING
CLINIC INC
x CITY GRANT PROGRAMS HUMAN SERVICES $12,031,905 $15,663,846 $11,291,184
BAKER PLACES INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $11,851,916 $12,620,056 $11,627,323
PROGRESS FOUNDATION x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $7,746,335 $11,763,095 $12,274,650
WALDEN HOUSE INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $8,970,983 $11,306,635 $9,538,259
Aside from the California Academy of Sciences, all of the top non profits funded by the city deal primarily with mental illness, substance abuse, and homelessness. Only Randy Shaw and Tenderloin Housing Clinic refuses to admit that he does pretty much the exact same thing as Progress Foundation and Walden House. Also the only one of the top five lacking the word ‘professional”, mostly because THC does not employ certified professionals like Walden House and Progress Foundation, yet they deal with nearly identical populations
the following is all non profits funded by the city that are over 1 million dollars. FY = fiscal year for the index
Vendor Names Non ProfitTypes of
Goods and Services Departments
FY 2006-07 FY 2007-08 FY 2008-09
ASIAN AMERICAN
RECOVERY SERVICES INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $8,329,110 $7,289,104 $6,810,443
ASIAN ART MUSEUM
FOUNDATION
x OTHER CURRENT
EXPENSES
ASIAN ART MUSEUM $1,728,747 $1,732,884 $1,651,306
BAKER PLACES INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $11,851,916 $12,620,056 $11,627,323
BAYVIEW HUNTERS PT
FNDTN FOR COMM
IMPROV
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $5,602,960 $5,720,779 $3,968,980
BLOOD CENTERS OF THE
PACIFIC
x HOSPITAL; CLINICS &
LABORATORY SUPPLIES
PUBLIC HEALTH $3,358,979 $3,172,487 $2,810,479
BRIDGE HOUSING CORP x OTHER SUPPORT & CARE
OF PERSONS
MAYOR $1,779,963 $1,948,487 $570,944
C V E INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,827,256 $1,981,256 $1,527,107
CALIFORNIA ACADEMY OF
SCIENCES
x PROFESSIONAL &
SPECIALIZED SERVICES
DEPARTMENT OF PUBLIC
WORKS
$66,974,017 $18,280,466 $2,767,359
CATHOLIC CHARITIES
CYO
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $2,153,817 $2,414,423 $2,317,350
CATHOLIC HLTHCR WST
DBA ST MARYS MED CTR
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,650,283 $1,117,425 $905,355
CHINATOWN COMMUNITY
DEVELOPMENT CENTER
x OTHER SUPPORT & CARE
OF PERSONS
MAYOR $4,379,123 $406,335 $687,646
COMMUNITY AWARENESS
& TREATMENT SVCS INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $4,768,865 $6,113,768 $5,706,838
COMMUNITY HOUSING
PARTNERSHIP
x CITY GRANT PROGRAMS HUMAN SERVICES $1,152,061 $2,358,996 $1,893,157
COMMUNITY WORKS x CITY GRANT PROGRAMS SHERIFF $1,396,929 $1,229,367 $340,783
COMPASS COMMUNITY
SERVICE
x CITY GRANT PROGRAMS HUMAN SERVICES $1,636,265 $3,213,153 $2,828,620
CONARD HOUSE INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $5,200,169 $5,932,418 $5,356,244
CORPORATION OF THE
FINE ARTS MUSEUMS
x OTHER CURRENT
EXPENSES
FINE ARTS MUSEUM $4,484,627 $2,521,452 $3,848,805
DELTA DENTAL PLAN OF
CALIFORNIA
x PROFESSIONAL &
SPECIALIZED SERVICES
HEALTH SERVICE SYSTEM $1,601,737 $1,454,738 $1,243,973
EDGEWOOD CENTER FOR
CHILDREN AND FAMILES
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $3,520,694 $3,774,494 $2,737,000
EPISCOPAL COMMUNITY
SVCS OF S F INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,991,417 $1,698,287 $1,369,674
FAMILY SUPPORT SVCS
OF THE BAY AREA
x CITY GRANT PROGRAMS HUMAN SERVICES $1,452,952 $1,154,955 $1,182,799
GOODWILL INDUST OF S F
SAN MATEO & MARIN
x CITY GRANT PROGRAMS HUMAN SERVICES $1,137,947 $1,532,504 $1,200,439
HAIGHT ASHBURY FREE
CLINIC INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $8,799,180 $10,862,828 $7,450,151
HAMILTON FAMILY
CENTER
x CITY GRANT PROGRAMS HUMAN SERVICES $3,242,193 $3,448,472 $2,878,996
HOMELESS PRENATAL
PROGRAM
x CITY GRANT PROGRAMS HUMAN SERVICES $1,185,269 $1,577,729 $1,265,894
HORIZONS UNLIMITED OF
SF
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,188,167 $1,067,503 $882,953
INSTITUTE ON AGING x CITY GRANT PROGRAMS HUMAN SERVICES $1,082,416 $2,979,958 $3,137,061
INSTITUTO FAMILIAR DE
LA RAZA INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $2,171,947 $2,604,985 $2,144,672
JAPANESE COMMUNITY
YOUTH COUNCIL
x CITY GRANT PROGRAMS CHILDREN; YOUTH & THEIR
FAMILIES
$4,857,605 $5,438,709 $5,822,020
JELANI HOUSE INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,757,044 $2,084,970 $1,439,948
LARKIN STREET YOUTH
CENTER
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,798,533 $1,905,402 $1,948,584
LARKIN STREET YOUTH
CENTER
x CITY GRANT PROGRAMS HUMAN SERVICES $2,859,189 $2,738,244 $3,021,659
LATINO COMMISSION x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,491,933 $1,383,211 $1,338,734
MAITRI AIDS HOSPICE x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,162,829 $741,082 $1,085,773
MEALS ON WHEELS x CITY GRANT PROGRAMS HUMAN SERVICES $3,019,443 $2,543,786 $2,856,577
MISSION COUNCIL ON
ALCOHOL
ABUSE/SPANISH
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,014,558 $942,108 $847,662
MISSION NEIGHBORHOOD
HEALTH CENTER
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,757,277 $2,441,472 $2,002,432
NEW LEAF SERVICES FOR
OUR COMMUNITY
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,697,193 $2,117,610 $1,679,383
P H F E MANAGEMENT
SOLUTIONS
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,479,140 $3,039,455 $2,130,149
POSITIVE RESOURCE
CENTER
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,133,063 $1,549,969 $1,300,719
PRIVATE INDUSTRY
COUNCIL OF S F INC
x CITY GRANT PROGRAMS HUMAN SERVICES $2,657,716 $1,802,073 $0
PROGRESS FOUNDATION x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $7,746,335 $11,763,095 $12,274,650
PROJECT OPEN HAND x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,110,054 $1,277,537 $1,095,686
PROJECT OPEN HAND x CITY GRANT PROGRAMS HUMAN SERVICES $1,262,371 $1,141,103 $1,048,462
RICHMOND AREA MULTISERVICES
INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $5,959,252 $8,647,470 $7,056,752
S F CONVENTION &
VISITORS BUREAU
x PROFESSIONAL &
SPECIALIZED SERVICES
ADMINISTRATIVE SERVICES $7,305,022 $9,116,310 $6,557,063
SAN FRANCISCO AIDS
FOUNDATION
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $4,885,447 $6,900,876 $6,103,391
SAN FRANCISCO
CONSERVATION CORPS
x CITY GRANT PROGRAMS MAYOR $1,098,145 $1,073,840 $941,503
SAN FRANCISCO
PRETRIAL DIVERSION
PROJECT
x CITY GRANT PROGRAMS SHERIFF $1,672,625 $2,373,924 $2,943,331
SAN FRANCISCO STATE
UNIVERSITY
x CITY GRANT PROGRAMS CHILDREN; YOUTH & THEIR
FAMILIES
$2,115,967 $1,904,657 $650,613
SAN FRANCISCO STUDY
CENTER INC
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $4,087,241 $2,548,862 $2,973,769
SAN FRANCISCO
SYMPHONY
x PROFESSIONAL &
SPECIALIZED SERVICES
ARTS COMMISSION $1,506,471 $1,633,039 $1,773,997
SAN FRANCISCO
ZOOLOGICAL SOCIETY
x PROFESSIONAL &
SPECIALIZED SERVICES
RECREATION AND PARK
COMMISSION
$4,120,000 $4,120,000 $3,776,667
SENECA CENTER x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $5,137,436 $5,370,847 $6,240,712
SHANTI PROJECT x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,503,938 $1,526,201 $1,185,296
ST VINCENT DE PAUL
SOCIETY OF SAN FRANCI
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,575,992 $1,427,926 $1,298,942
TENDERLOIN AIDS
RESOURCE CENTER
x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $2,053,936 $339,645 $225,924
TENDERLOIN AIDS
RESOURCE CENTER
x CITY GRANT PROGRAMS HUMAN SERVICES $1,706,694 $529,983 $0
TENDERLOIN HOUSING
CLINIC INC
x CITY GRANT PROGRAMS HUMAN SERVICES $12,031,905 $15,663,846 $11,291,184
THE GARDEN PROJECT x CITY GRANT PROGRAMS SHERIFF $1,177,870 $671,711 $468,483
TIDES CENTER x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $1,325,383 $2,794,603 $3,447,168
UNITED COUNCIL OF
HUMAN SERVICES INC
x CITY GRANT PROGRAMS HUMAN SERVICES $1,755,483 $1,992,310 $548,882
WALDEN HOUSE INC x PROFESSIONAL &
SPECIALIZED SERVICES
PUBLIC HEALTH $8,970,983 $11,306,635 $9,538,259
WU YEE CHILDREN’S
SERVICES
x CITY GRANT PROGRAMS CHILDREN AND FAMILIES
COMMISSION
$3,253,389 $4,467,398 $1,950,569
WU YEE CHILDREN’S
SERVICES
x CITY GRANT PROGRAMS CHILDREN; YOUTH & THEIR
FAMILIES
$2,384,647 $2,328,449 $2,137,991
Y M C A OF SAN
FRANCISCO
x CITY GRANT PROGRAMS CHILDREN; YOUTH & THEIR
FAMILIES
$3,347,217 $4,638,765 $4,778,806
Compare with the 2007 federal form 990