The changes in rackets, strength training, and fitness make it hard to compare eras, but I would put Serena 1st. Her biggest rival, for a while, was her sister. (19-12 all time back Venus head to head). How hard is that?
Martina would probably be my #2. She had to deal with a lot off the court as she is one of the first athletes in their prime who I remember being "out", and a lot of people didn't like her for that, plus, her biggest rival was America's Sweetheart, Chrissy.
Martina kind of started the transition to a more physical game of tennis. (My recollection is that she was really the first woman to rely on serve and volley). Chris may have been better technically, but Martina's power and athletic superiority led he past Chris.
Regardless off all of the GOAT talk, Serena went out with the heart of a champion tonight. I hope she stays retired as I don't think it will get better than tonight. She didn't play poorly and lost. She played great, but got beat, and that's ok.