DC has always had Wonder Woman as their undisputed #1 female character from the 1940s through today (though Harley Quinn is now a clear- cut #2 since 2010).

What about Marvel?
They have no equivalent to Diana, but I do think I've the decade, different women have worn the crown.

I'd say:

1960s: Susan Storm-Richards
1970s: ???
1980s: Jennifer Walters
1990s: Ororo Munroe
2000s: ???
2010s: Carol Danvers

I may be off, so please provide your own lists.