(Having been asked which of the stories I thought was real.)
In a literal sense, I'm not sure - could be either the 'realistic' one he tells at the end or the 'fantastic' one which makes up most of the novel.
I'd be strongly inclined to say the realistic one were it not for the bones in the boat which no one is able to identify (and so which may belong to the meerkat-y creatures from the island, suggesting that the fantastic one may also in a sense be real).
Without the bones, I would read it as: the realistic story is what actually happened in the external world, but in some internal or figurative sense, the fantastic story is how it really was for Pi, and that internal/figurative (ie, subjective) sense is just as valid/true (it's a better story; so it is for God; etc).
But with the bones, I think the ambiguity is a weakness of the novel (although some would call it a strength). There's nothing wrong with leaving the status of a narrative open to question and having its ending ambiguous; however, it should be possible to articulate exactly where the ambiguity lies. Here, the interesting question about the respective statuses of the realistic and fantastic stories is muddied for no good reason by the crossing-over between the two possibilities which results from the bones (which are apparently inexplicable except if you accept the fantastic story is the real one).
Another possibility, of course, is that any attempt to read Life of Pi literally, misses the point of the novel - the text wilfully mingles the apparently real and the apparently fantastic. On this reading, neither story is 'real' (or they both are). But if that's what the text sets out to do, it needs to earn or justify that mingling far better than it actually does, so it would still be unsatisfactory for me.
