Firstly, I think it should be added that global championship marathons don't hold as much weight as, say, a 1500m global title would. Marathoners race sparingly and their main chance of raking in the cash is with the big city marathons. Whether they are also fit for the glocal championships marathons can sometimes be hit and miss. Also, big city marathons often have much higher quality fields, as there is no limit on the number of athletes from each nation (namely Kenya, Ethiopia, Japan) that can compete in them. Of course global titles are important, but in some instances, it is extremely feasible that the greatest marathon runners of all time could end up with no global title whatsoever.
Anyway, my list...
1. Paula Radcliffe
Has won all the marathons she has completed. Top three clockings of all-time, four of the top five times of all-time. Three time London winner with other other big city marathons (NY and Chicago) to boot. Has beaten all of the other top current marathoners at least once (Ndereba, Okayo, Kiplagat, Yingjie, Dita, Chepkemei, etc, etc...). Very much a pioneer of women's distance running and will go down in history as a marathon legend. Only thing lacking so far is a global title, but when she does get one of these, then her place atop the all-time greatest rankings will be unquestionable.
2. Catherine Ndereba
Good championships record (WCh gold, OG silver). 50% winning record and has finished in the top two in all of her marathons since 2000. Can hang with a fast pace, or can treat it more like a race with lethal closing strength. Four-time Boston winner, 2-time Chicago winner. Was ranked behind Radcliffe mainly based on their head-to-heads.
3. Grete Waitz
Another pioneer of women's marathon running. First woman below 2:30, and had four world records. She won the world champs marathon, and had an Olympic silver to boot (much like Ndereba). Plenty of big-city marathon wins, however she falls back somewhat on the fact that she competed in the event when it was still quite young, and her PR in the marathon seems rather weak nowadays (although her 1500m and 3000m times would still be classed as very respectable today).
Others:
4. Ingrid Kristiansen
5. Rosa Mota
6. Naoko Takahashi
7. Katrin Dörre
8. Joan Benoit
9. Tegla Loroupe
10. Uta Pippig