Both are used, but on is hugely predominant. This is to be expected: on is the normal preposition when talking about specific communications media that operate through transmission: on TV, on the radio, on the phone - and thus, on the Web, on Facebook, on Youtube - and on the Internet. Metaphorical expressions reinforce the usage: one surfs on the Internet. And the governing organizations, such as ICANN, all talk in this way.
The competition from in has come from the physical forms of communication where one can look 'inside'. So, one finds something in a book, in a magazine, in a newspaper, and so on. The metalanguage of the print medium early influenced the description of online outputs, with talk of 'pages', and the like, so it's easy to see how an alternative usage would develop. And if one looks in a book, then there is an analogy motivating doing something in a location named after a book - Facebook. This is reinforced by the actual process of opening up a website and looking inside it to find information.
I use both prepositions, in this respect, depending on the semantics of what I have in mind. I say to people that they will find something on my website and also in my website, depending on whether I am thinking of the website as a single location or as a container of data. Same applies to blogging: you will find this post on my blog as well as in my blog. This isn't the first time such an alternative has emerged in English: one can find a place on a map of Britain or in a map of Britain.
Two other factors have reinforced the growth of in. We see it when people think of the Internet as a physical phenomenon, such as when writing programmes - another application of the 'looking inside' motif. I'm less certain about the second point, but I have the impression that in has become the item of choice among non-native English-users who are uncertain of which preposition to use, and who see conflicting usage online. I'd be interested to hear opinions on this point.