Background and Context

The Oxford Research Encyclopedias: American History offers numerous articles reviewing specialized topics.  Each article has sections on Discussion of the Literature and on Primary Sources, together with a Further Reading bibliography and footnotes.

This gives city by city overviews:
Encyclopedia of urban cultures : cities and cultures around the world, edited by Melvin Ember and Carol R. Ember.  Danbury, Conn.: Grolier, 2002.  4 v.
HOLLIS Record with online access

The language of cities; a glossary of terms, by Charles Abrams.. NY: Viking Press, 1971, 365 p.
HOLLIS record with online access

Encyclopedia of the city, ed. by Roger W. Caves. London ; NY: Routledge, 2005, 564 p.

Encyclopedia of American urban history, ed. by David Goldfield. Thousand Oaks: Sage Publications, 2007. 2 v.

Historic cities of the Americas: an illustrated encyclopedia, by David F. Marley. Santa Barbara, Calif.: ABC-CLIO, 2005. 2 v.
HOLLIS record with online access

The urban politics dictionary, by John W. Smith, John S. Klemanski. Santa Barbara, Calif.: ABC-CLIO, 1990, 613 p.
HOLLIS record with online access

Encyclopedia of urban America: the cities and suburbs, ed. by Neil Larry Shumsky. Santa Barbara, Calif.: ABC-CLIO, 1998, 2 v.
HOLLIS record with online access

Encyclopedia of urban studies, ed. by Ray Hutchison. Thousand Oaks, Calif.: SAGE Publications, 2010. 2 v.
HOLLIS record with online access

Encyclopedia of urban planning, ed. by Arnold Whittick. Huntington, NY: R. E. Krieger Pub. Co., 1980, 1974, 1218 p.

Encyclopedia of world cities, by Immanuel Ness. Chicago : Fitzroy Dearborn, 1999, 739 p.
Widener | RR 4201.72

Particular Cities

Boston: a chronological & documentary history, 1602-1970, by George J. Lankevich. Dobbs Ferry, NY: Oceana Publications, 1974, 152 p.
HOLLIS record with online access

Boston A to Z, by Thomas H. O'Connor. Cambridge, MA: Harvard University Press, 2000, 370 p.
HOLLIS record with online access

The encyclopedia of Cleveland history, by David D. Van Tassel. 2nd ed. Bloomington: Indiana University Press, 1996, 1165 p.
HOLLIS record with online access

The encyclopedia of New York City, ed. by Kenneth T. Jackson. 2nd ed. New Haven: Yale University Press ; NY: New-York Historical Society, 2010, 1561 p. 
HOLLIS Record
Internet Archive Full Text

The encyclopedia of New England: the culture and history of an American region, ed. by Burt Feintuch and David H. Watters. New Haven: Yale University Press, 2005, 1564 p.
Andover-Harv. Theol | Ref. | F4 .E53 2005
Lamont | REFERENCE | F4 .E53 2005
Map Coll (Pusey) | REF MAP-LC | F4 .E53 2005 f
Widener | WID-LC | F4 .E53 2005

Chicago neighborhoods and suburbs: a historical guide, by Ann Durkin Keating. Chicago: University of Chicago Press, 2008, 329 p.
Loeb Design | F548.18 .K43 2008
Widener | Harvard Depository | F548.18 .K43 2008

The encyclopedia of Chicago, ed. by James R. Grossman, Ann Durkin Keating, Janice L. Reiff. Chicago : University of Chicago Press, 2004, 1117 p.
Loeb Design | F548.3 .E53 2004
Widener | WID-LC | F548.3 .E53 2004

The encyclopedia of Cleveland history, by David D. Van Tassel. 2nd ed. Bloomington: Indiana University Press, 1996, 1165 p.
Widener | WID-LC | F499.C657 E53 1996

Los Angeles A to Z: an encyclopedia of the city and county, by Leonard Pitt and Dale Pitt. Berkeley: University of California Press, 1997, 603 p.
Loeb Design | F869.L84 P58 1997
Widener | WID-LC | F869.L84 .P58 1997

The encyclopedia of New York City, ed. by Kenneth T. Jackson. 2nd ed. New Haven: Yale University Press ; NY: New-York Historical Society, 2010, 1561 p.
Widener | RR 3642.15

Encyclopedia of San Francisco (San Francisco Museum & Historical Society)

Virtual Museum of the City of San Francisco