Wow that is a tough one. Most Silver Age Marvels are based in NY but DC has always used fictitous cities. Here is a list from the GCD that might be available here. I think most of them are
Smash Comics #5
Mystery Men #8
Rance's New York Adventure
Rance Keane / story / 4 pages Feature Comics (1939 series) #33
June 1940 Quality Comics
The Secret New York Sub Base
Red Torpedo / story / 5 pages Crack Comics (1940 series) #4
August 1940 Quality Comics
"Into New York harbor steams the 'Beggars' Yacht..."
Inspector Dayton / story / 7 pages Jumbo Comics (1938 series) #19
September 1940 Fiction House
New York Championship Bout
Kid Dixon / story / 5 pages National Comics (1940 series) #3
September 1940 Quality Comics
Milk Shortage Threatens New York
Green Mask / story / 8 pages Green Mask, The (1940 series) #2
Fall 1940 Fox
At Army Intelligence headquarters in New York...
Don Davis / story / 6 pages Startling Comics (1940 series) #7
May 1941 Standard
The Bombing of New York
K-51 Spies At War / story / 5 pages Wonderworld Comics (1939 series) #26
June 1941 Fox
"The office of Tony the Tornado -- notorious New York taxi-cab racketeer..."
The Twister / story / 8 pages Blue Bolt Comics (1940 series) #v2#2 [14]
July 1941 Novelty Press
I'd like you to go to the Collegiate League meeting in New York, Dan!
Dan Duffy / story / 7 pages Thrilling Comics (1940 series) #18
July 1941 Standard
Neon the Unknown / story / 5 pages Hit Comics (1940 series) #14
August 1941 Quality Comics
The Plot To Blow Up New York City
Neon the Unknown / story / 5 pages Hit Comics (1940 series) #15
September 1941 Quality Comics
"In the drugged atmosphere of her exotic New York apartment, Nagana..."
The Queen of Evil / story / 6 pages Fantastic Comics (1939 series) #23
November 1941 Fox
[Scene: Deportation Headquarters, New York City!
Blue Bolt / story / 6 pages Blue Bolt Comics (1940 series) #v2#6 [18]
November 1941 Novelty Press
Enroute from Cape Town, South Africa, to New York City"
The Owl / story / 5 pages Popular Comics (1936 series) #75
May 1942 Dell
"Antone Thanie--A leading New York jeweler..."
The Voice the Invisible Detective / story / 8 pages Popular Comics (1936 series) #75
May 1942 Dell
New York Under Fire
Crimebuster / text story / 2 pages Daredevil Comics (1941 series) #10
May 1942 Lev Gleason
Back In New York
Sergeant Boyle / story / 8 pages Pep Comics (1940 series) #31
September 1942 Archie
Case 2 Bombers Over New York City
G-2 / story / 9 pages National Comics (1940 series) #28
January 1943 Quality Comics
Adventure with the Lions in New York City
text story / 2 pages Blue Beetle (1942 series) #22
June 1943 Holyoke
Bombs Over New York City
Bald Eagle / story / 7 pages Air Fighters Comics (1941 series) #v1 #10
July 1943 Hillman
The Smashing Case of Voodoo in New York
Crime Reporter / story / 7 pages Blue Beetle (1942 series) #23
July 1943 Holyoke
The Nazi Knights of New York
Minute Man / story / 13 pages Master Comics (1940 series) #44
November 1943 Fawcett
The Bombing of New York
American Eagle / story / 10 pages Exciting Comics (1940 series) #30
December 1943 Stanard
"Our two heroes are now in New York -- you'll remember..."
Krisko and Jasper / story / 5 pages Blue Bolt Comics (1940 series) #v4#11 [47]
June 1944 Novelty Press
Her Secret Visit To New York
Mary Marvel Enterprises, Inc. / advertisement / 1 page Whiz Comics (1940 series) #57
August 1944 Fawcett
The Secret Visit To New York
Mary Marvel / advertisement / 1 page Wow Comics (1940 series) #28
August 1944 Fawcett
"From a voyage of discovery through New York..."
Stuart Taylor / story / 5 pages Jumbo Comics (1938 series) #73
March 1945 Fiction House
"One bright, gay spring morning on a pier in New York City..."
Harbor Patrol / story / 7 pages Seven Seas Comics (1946 series) #2
July 1946 Leader Enterprises / Universal Phoenix Features
The New York Cattle Rustlers
Young Robinhood / story / 7 pages Boy Comics (1942 series) #31
December 1946 Lev Gleason
New York City: Part II
Cities of Destiny / story / 3 pages True Comics (1941 series) #62
July 1947 Parents' Magazine Press
Bateese and Balonki Visit New York
Bateese and Balonki / story / 6 pages Joe Palooka Comics (1945 series) #16
January 1948 Harvey
His Peculiar Trip To New York (Part 1)
Humphrey / story / 10 pages Humphrey Comics (1948 series) #1
October 1948 Harvey
Chief Thomas B. Moriary Long Beach, New York
Our Police Hall of Fame / text article / 2.5 pages Crime Does Not Pay (1942 series) #74
April 1949 LevGleason
New York's Gunmen Feared Captain Pat McVeigh
Captain Pat McVeigh / story / New Heroic Comics (1946 series) #56
September 1949 Eastern Color
"Lester Broderick, New York City, was arrested and fined $25"
On the Level / filler / 1 page Crime Does Not Pay (1942 series) #88
June 1950 Lev Gleason
The Battle of New York
story / 8 pages Airboy Comics (1945 series) #v7 #5
June 1950 Hillman
The New York Yankees
filler / 1 page Thrilling True Stories Of The Baseball Yankees (1952 series) #[nn]
1952 Fawcett
New York to Paris on Wheels
story / 6 pages Hot Rod and Speedway Comics (1952 series) #2
September - October 1952 Hillman
Chop Chop In New York
Chop Chop / story / 4 pages Blackhawk (1944 series) #58
November 1952 Quality Comics
Weekend in New York
story / 7 pages Pictorial Romances (1950 series) #19
May 1953 St. John
The Claw Invades New York City
Rocky X / story / 6 pages Boy Comics (1942 series) #90
June 1953 Lev Gleason
"Spark up if you want to be a catcher!" said "Yogi" Berra, star catcher, New York Yankees
advertisement / 1 page Looney Tunes and Merrie Melodies (1950 series) #142
August 1953 Dell
Secret Agent in New York
Ed Wells, U.S. Secret Service / story / 7 pages Danger (1953 series) #6
November 1953 Comic Media
The Indians of New York State
text story / 1 page Roy Rogers Comics (1948 series) #89
May 1955 Dell
Chop Chop In New York
Chop Chop / story / 4 pages Blackhawk (1944 series) #90
July 1955 Quality Comics
Secret Agent From New York
story / 7 pages Johnny Dynamite (1955 series) #11
August 1955 Charlton