A thread about interesting comic book female superheroes from the Golden Age of Comic Books (circa 1938-1955) that you've come across, but aren't from DC or Marvel and don't seem to be particularly well-known.
One that interested me (and is quite possibly the first comic book character to use an alter ego of a superpowered costumed crimefighter) is the Magician from Mars, from Centaur Publications' Amazing-Man Comics. A half-human/half-Martian who gains reality-warping powers after being exposed to cathode tube rays and, after losing her parents, is raised by her aunt, who turns out to be the leader of a villainous organization.
Also, I'll put a list I put together here which includes many non-DC/Marvel heroes too:
1939 - Crimson Rider, Golden Amazon, Magician from Mars
1940 - Alice of the Winged People, Black Widow (Timely Comics), Fantomah, Headless Horseman, Invisible Scarlet O'Neil, Lady Luck, Mighty Woman, Miss X, Red Tornado, Woman in Red
1941 - Black Cat, Black Widow (Holyoke Publishing), Blue Lady, Bulletgirl, Flame Girl, Hawkgirl, Kitten, Lady Fairplay, Lady Satan (Harry 'A' Chesler), Madame Strange, Margo the Magician, Miss America (Quality Comics), Miss Fury, Miss Victory, Mother Hubbard, Nelvana of the Northern Lights, Owl Girl, Pat Patriot, Phantom Lady, Ranger Girl, Rocketgirl, Silver Scorpion, Spider Queen, Super Ann, USA the Spirit of Old Glory, Wildfire, Wonder Woman
1942 - Black Angel, Blonde Bomber, Girl Commandos, Liberty Belle, Lightning Girl, Mary Marvel, Señorita Rio, Spider Widow, The Wing
1943 - Black Orchid (Harvey Comics), Lady Satan (Harvey Comics), Miss America (Timely Comics), Miss Patriot, Superwoman
1944 - Black Orchid (Consolidated Book Publishers), Black Venus, Catgirl, Diana the Huntress, Dotty Whirlwind (aka Dotty Virvelvind), Miss Espionage, Purple Tigress, Spider Woman, Veiled Avenger, Will O' The Wisp
1945 - Comandette, Firehair, Freckles Marvel, Ghost Woman, Mysta of the Moon, Polka-Dot Pirate, Yankee Girl (Four Star Publications)
1946 - Blonde Phantom, The Flame, Front Page Peggy, Futura, Golden Girl (Spark Publications), Lady Fantax, Magga the Magnificent, Miss Fear, Miss Masque, The Torch (aka la Antorcha)
1947 - Acromaid, Atoma, Black Canary, Electro Girl, Iron Lady, Marvel Maid, Moon Girl, Namora, Phantom Maid, Undercover Girl, Vampire, Varga, Yankee Girl (Harry 'A' Chesler)
1948 - The Cat (aka de Kat), Elektra, Gimmick Girl, Golden Girl (Timely Comics), Lady Danger, Miss Devil (aka Miss Diavolo), Sun Girl, Val Venture, Venus
1949 - The Queen of Spades (aka la Dama di Picche), Supergirl
1950 - The Avenging Plainswoman (aka la Llanera Vengadora), Calamity Kate, Darna, The Silent Three, Starlight, TNT Tina
1951 - Black Phantom, Corsair Queen, Doll Girl
1952 - Galaxy Gals
1953 - Sri Asih, Zina of Koroka
1954 - Princess Bintang (aka Putri Bintang), Tomboy