It might be better for you to email me on this one, actually, so I can hear details on what the editorial vision sounds like from each. You're welcome to. But from what I can tell on this thread, and from what I know of the houses, I'd probably go with any of the top three, really. Each has their own advantage.
Little, Brown is a much smaller house than Scholastic and will probably give you a lot of attention. Houghton is Boston-based, so it's out of the New York crowd and has a slightly different vision, but most of their editors concentrate on picture books as far as I last knew. The last editor I knew there in trade left last year, so I have less personal connection to what their editorial vision is as far as fantasy goes, and the only reason I think of them in connection with fantasy at all is because of LotR. But Houghton does also have a really small trade department--meaning lots of personal attention to the books, because their line is smaller--but has the monetary backing of the whole company as far as promotion goes.
Scholastic, though, has a *machine* as far as promotion goes, and who knows, with being such a large house, they probably are able to let editors not be so swamped as a little house might be (i.e., fewer books per editor). But they made a whole bunch of cuts just a couple months ago, so that may not be true.
Tor is... well, they're a new imprint, so they could really use the boost of a hit for Starscape, but their editorial vision doesn't really match the feeling of Alcatraz to me. Most of what I've seen coming from Starscape is high fantasy with the standard tropes, published in original paperback. They released a YA fantasy anthology last year purporting to be "new" fantasy that had no story newer than 2000, and most were reprints from adult authors in the 80s. Not one YA author in the whole anthology that wasn't primarily an adult author.
I mean, part of me says that you'd want to help the new imprint out, but if you're being offered big money by the others, that means they're really going to believe in it and promote it. If it's even half the figure that the Opal Mehta book that everyone's talking about right now, you'd be guaranteed a lot of press, reviews, etc. Before the plagiarism thing hit, Opal Mehta was being talked about on all the library listservs, librarians asking where to shelve it, what people thought of it, etc.
For me, it comes between the top three's editorial vision. If they're really close on per-book, I wouldn't worry about whether it's 4 or 6. If it does well, they'll contract you for more, and finding a great editor that you really feel you'll work well with will be worth the difference in the books if you pick the one who only is offering 4.
But like I said, I'd be interested in hearing details about what the editors said editorially.
Oh, and which imprint of Scholastic are we talking about? That's important. If it's Arthur Levine, that trumps everything. Go with Arthur.