I'll start with the four I think are the very best of these.
Floriole - near the Fullerton stop on the Red/Brown/Purple lines
Alliance Bakery - near the Division stop on the Blue line
Vanille Patisserie - 3 locations; French Market is near all L lines; Lincoln Park is near the Sedgwick stop on the Brown/Purple lines; Lakeview is near the Belmont stop on the Red/Brown/Purple lines
Southern France - near the Sheridan stop on the Red line
Toni Patisserie - Loop location is near all L lines
Maison Parisienne - near the Belmont stop on the Red/Brown/Purple lines
Jennivee’s Bakery - near the Belmont stop on the Red/Brown/Purple lines
Bittersweet Pastry - near the Belmont stop on the Red/Brown/Purple lines
La Boulangerie - 2 locations; Lakeview is near the Belmont stop on the Red/Brown/Purple lines; Ravenswood is near the Damen stop on the Brown line
Chiu Quon Bakery - near the Argyle stop on the Red line
Patisserie P - near the Argyle stop on the Red line
Cellar Door Provisions - near the Logan Square stop on the Blue line
Delightful Pastries - 2 locations; French Market is near all L lines; Jefferson Park is near the Jefferson Park stop on the Blue line
La Fournette - 2 locations; Old Town is near the Sedgwick stop on the Brown/Purple lines; Lakeview is near the Fullerton stop on the Red/Brown/Purple lines
Hendrickx Bakery - near the Chicago stop on the Red line
Since you're the pie lady, you're probably already familiar with:
Bang Bang Pie - 2 locations; Ravenswood is near the Damen stop on the Brown line; Logan Square is near the California stop on the Blue line
Hoosier Mama Pie - 2 locations; Chicago is between the Chicago and the Division stops on the Blue line; Evanston is near the Main stop on the Purple line
Speaking of Evanston, I know you didn't ask about the Purple line, but it's an extension of the Red line, and in addition to Hoosier Mama, you have...
Al's Deli near the Noyes stop on the Purple line (their cookies are awesome)
Patisserie Coralie near the Davis stop on the Purple line
Bennison's near the Davis stop on the Purple line
Hewn near the Dempster stop on the Purple line
And then there are the donut places, most of which are near L stops:
FirecakesGlazed & InfusedDo-Rite DonutsDoughnut VaultStan's DonutsBeaver's Donuts