Jingle - from a story standpoint, Lyanna is far and away the best candidate as the KotLT.
If the KotLT is Howland, we have a nice little vignette with little relevance or importance to the rest of the story, as far as we can see. The only importance of the KotLT tale in this case are incidental mentions in the tale of information we have already from other sources (eg, that Ned and Ashara had a mutual attraction, or that Lyanna and Rhaegar did).
On the other hand, if it's Lyanna, it explains neatly why Rhaegar gave her the rose crown. Remember, Lyanna and Rhaegar had not (so far as we know) even spoken before he does this - and I'm sure someone would have mentioned it if they had. The idea that he gave her the crown because he knew she was the KotLT explains this impulsive - and politically foolish - act.
If Lyanna is the KotLT, this also explains how Lyanna and Rhaegar met - he is sent to find the KotLT, discovers it is this spirited girl, and falls in love with her bravery etc. Much more satisfying, from a story point of view, than Rhaegar falling in love with a girl at first sight. He's not made out to be a superficial guy.
And if it's Lyanna, then the KotLT story is key to explaining the whole set of events that followed the Harrenhal tourney.
From an internal story logic point of view, it fits also. We
know that Lyanna is good with a sword: she beats three squires with a tourney sword. Even
Sandor has trouble with multiple opponents of lesser skill: in fact, we see only four people
in the whole series who take on multiple opponents of lesser skill and win easily - Garlan and Loras Tyrell (and Loras was enraged by Renly's death), Syrio, and Lyanna. So Lyanna is not just familiar with which end of a sword is which: she's
good.
We can assume, from remarks Ned makes, that she was also familiar with riding and jousting skills.
Howland, OTOH, has no particular skill with sword and can hardly ride at all, let alone joust. For Howland to be the KotLT, he has to get his tourney skills from nowhere, in a day. (Yes, he later fights (and survives) at the ToJ: but I suspect there's more to that tale than meets the eye. And besides, that's with different weapons.) Magic is the only explanation that can do this for him, and I don't think that fits the 'tone' of how magic is used in the series.
We also know that Lyanna has a fierce and combative nature. Howland does not, going from the only information we have on him (the tale of the KotLT itself). He avoids fighting when he can. So personality-wise, it makes more sense for it to be Lyanna who comes up with the idea.
Then there's stuff I've already mentioned: the disguise, the voice, the fact that Ned doesn't tell the tale (and that this seems odd to Jojen and Meera).
Frankly, I don't see anything but circumstantial evidence for the KotLT being Howland either, btw. That's kind of why the identity of the KotLT is still a mystery, see?
There's only circumstantial evidence for anyone.
But I will say that I am surer that Lyanna was the KotLT than I am of practically any other 'theory'. I am as sure of that as I am that Jon is Lyanna's son - surer than I am of who poisoned Joff, even, and LF admitted that one. It is the one theory I don't doubt, and believe you me I've heard a few.