Well, I don't have either one. I have a Toyota 4-Runner. And Arkydo is right, the Tundra is rated the best truck.
But as far as Hondas go, I've owned MANY. My dad also owns a Honda dealership. You cannot go wrong with a Honda. Its true. I have the same reservations as Jenn with the Element, we need more ground clearance and towing capacity. (We have a semi largish boat) I've thought about getting one for "my" car since hubby has the 4-Runner. But, it seems a little excessive. Anyway, I've driven them, and really like them. They're cute and spunky and have great cargo space. YOu can take out all of the seats quickly and easily which is awesome with the biguns. You can get the waterproof seats and floor, but that wasn't standard, it was an option, so check and see if the one you're looking at has those options.
All around, I say go with a Honda all the way. They're cleaner, better for the environment and very very well built!