I would have to say Spirit Tracks, by far. Phantom Hourglass did have some tough spots, mainly in the dreaded Temple of the Ocean King. I think also the first time or so, chasing the Ghost Ship was also a bit of a challenge. The first stage of the Bellum Battle was interesting as well, but Eox's fight just seemed a bit unfair in some sections, mainly trying to get his head.
Spirit Track's bosses and Phantom Hourglass's bosses were actually about equal, but Bellum was much more challenging as a boss than Malladus, especially in the final part. Both of the final sections of the final bosses were repetitive, but Bellum at least kept it interesting when he did the spin attack and started to make it harder; Malladus didn't really change anything at all. The bosses in both games were interesting, but Spirit Track's seemed to be more unique, while Phantom Hourglass's bosses felt a bit like a flash back to the past games like Wind Waker and A Link to the Past.
Dungeon wise, Spirit Tracks triumphs Phantom Hourglass. They made greater usage of the items inside of the dungeons and would allow you to use items from past dungeons better, rather than in Phantom Hourglass, where the whole dungeon is wrapped around one item. Overworld wise, Spirit Tracks also wins, because you have to be decisive or otherwise end up in a collision, whereas in Phantom Hourglass, you could easily navigate around. So, whether which one you think is harder depends on which parts of the game you're looking. Overall, however, I think Spirit Tracks wins.