Originally they all wore the same color masks in the comic book. It was the first videogames and the cartoon series that introduced the different color masks.
Somewhere in my apartment I have a few copies of the comic book in which they first appeared in color, it was an issue of Grimjack and Eastman and Laird did the backup series (Munden's Bar) in that issue and the turtles were in it. They all had red masks. The reason I have multiple copies is because that issue is semi-valuable, and I pulled several of them from a quarter bin at a comic store many years ago.