I think it is best to start looking for the answer on the metaphysical level.
The writers' purpose made this scene ambiguous as to leave uncertainty in the viewers' mind, and spark their imaginations. This distinction is even brought up explicitly by the characters themselves as they reflect on the scene as they are leaving. It seems that the writers were successful in accomplishing exactly what they wanted to.
Now, all of that said, one could examine the entire context and find some evidence for both claims.
Evidence that it was Latias
The girl did not say anything, and of course Latias can't speak. Now, of course Bianca could have simply decided to stay silent, but it seems awkward that if she were to make such an emotional and romantic advance that she'd say nothing. Consider these small phrases that would be appropriate (and seem awkward without): Thank you., I'll never forget you., I love you., etc.
She says absolutely nothing, most likely because she can't.
Throughout the movie, Latias is the one who shows an interest in Ash. In fact there is no signs of any chemistry at all between Ash and Bianca. If it is Bianca that kisses him, then perhaps she does so because she secretly likes Ash, but is to scared to show it, but doesn't want him to leave without a sign of affection to remember her by? Even that is pushing it. Considering the absurdity of it being Bianca, we must logically say it was Latias.
Ash mainly saved Latias who was in the greatest distress, and not really Bianca. Therefore Latias has good reason to want to thank Ash, at least more so than Bianca.
Evidence that it was Bianca
The piece of art was Bianca's. If it had been Latias that gave it to Ash, she basically would have had to have stolen† it from Bianca, which might have made her mad; this seems out of character for Latias.
† Of course Latias could have gotten explicit permission from Bianca, but this wasn't shown, so to support this theory we must enter the realm of pure speculation.
Regardless of who owns the piece of art, we must consider who made it. Bianca is the artist, since Latias can't paint. Why did she make a portrait of Ash in the first place? While she could have done it just for Latias, this seems awkward. Most likely this drawing was motivated through Bianca's own good will; though out of romantic, or perhaps just friendly interest remains to be seen.
Bianca's hat, which throughout the film was the only visible characteristic available to distinguish the two, is seem at home, implying that since she isn't using it, she must not be out, and thus the girl we see is Bianca. Of course we can't say this for sure since the girl doesn't grab it on her way out either. Again, this was probably done on purpose by the writers.
This isn't really directly perceptible evidence, but many find it odd that there could be a romantic scene between a human and a Pokemon. This relationship, of course, is not meant to be developed.
- It was Bianca trying to make them think she was Latias - Some speculate that Bianca purposely didn't wear her hat, nor speak, to make Ash think she was Latias. There is little reason to support this, other than perhaps Bianca was embarrassed to let him know how she felt, or the she wanted to thank him, but thought it would be more appropriate if they thought it was Latias expressing the gratitude.
Is there an official statement?
Official authorities have never clarified this up, and the only info Bulbapedia can offer is a restatement of what we already know:
...The conclusion of the film briefly sees her finishing a drawing. The drawing, which is of Ash and Pikachu, is given to Ash by either Bianca, who had left her hat on her easel, or Latias in the form of Bianca: which is the case is the subject of debate. When Ash received the sketch, the girl kissed him. Bianca is seen again in the credits drawing another sketch by the harbor.
-- Bianca (movie), Bulbapedia
Is there a general consensus?
I feel that in general most consider it to be Latias, simply because she showed interest in Ash throughout the film. A few polls have been conducted on a some forums, including:
Neither poll is truly scientific, but both give a good idea of the general gist of the matter.
In conclusion, there is evidence to support either case, and in following with what the writers wanted we are able to make up our own mind. Sometimes the imagination is able to put something in a way that no story ever could.