This poll needs a third option -- something like "no preference/it depends." Especially with interactive books, it really depends on the content. Some contents, like videos, might be better in landscape, but others, like some multiple choice quizzes I've seen, seemed to work better in portrait. As for regular books, it depends on where and how I'm sitting, if I have a stand or a pillow, and just what mood I'm in.
In other words, I don't much care which way I hold my iPad. Just like some games work in landscape and some in portrait, and I'm happy to turn my iPad to fit the game. I'm happy with interactive works that work either way, as long as the contents and design are good.