She won against Voldemort 'thrice times'!

^ No, the wording was that she and her husband defied Voldemort three times, not "won against". That can mean anything from questioned, challenged, refused, resisted, etc. Voldemort certainly didn't think both Lily and James would be much of a challenge against him as he attacked them both in Godric's Hollow by himself.

she had more heart & strength

I don't like Molly at all. Winning against Bella was luck!
Lily is a powerful witch and a brighter one than Mrs. Weasley.

It's kind of an unfair question, considering we got to know Molly much better than we did Lily. But I'm gonna have to go with Molly on this one simply because she totally pwned Bellatrix.

hello..defied voldy 3 times..

yeah, besides Molly killing Bella (which btw seemed unlikely at best, it really seemed like JK just put that in there so Molly could say her infamous line), she has never shown any real duelling ability. the only spells we know for sure she can cast are household ones for cleaning and whatnot. We know Lily was really skilled and clever so she definitely would have had the edge. though i can't see a reason for them to ever have duelled, unless Lily lived and she didn't want Harry to marry Ginny or something like that ;)

I don't think that Molly is weak or not powerful enough to kill Bellatrix. We've only seen her around the house, but you never know what's behind that homey wand wavering of hers.
But when it comes down to it, Lily was just a genius...

Molly winning agains Bellatrix was just some kind of error! Lilly's better!