I'm not done playing through all the games yet, but the way I'd rank them currently, I will agree that Wind Waker is the easiest, since I am currently playing through it (and have only played it partly once before) and haven't really encountered that much challenge (not that I dislike that, I like having a game I can be all confident about, and it still manages to be a lot of fun regardless).
I know Occarina of Time in and out, so although it does have some challenges that was harder first time around, it just has to take the spot of second easiest title.
Twilight Princess have some challenges, which were annoying, especially when playing the wii version (the carriage escort mission, for instance, or the bridge-top jousting). But some of the challenge go away when playing the Gamecube version, so it takes the middle spot for me.
Skyward Sword comes next, mainly because of the motion plus controls. It took me forever to get past the first Girahim encounter because Link just wouldn't move the way I was trying to. Had the game been released with a button-alternative, I'm sure I would feel differently.
Majora's Mask takes the top spot in most difficult for me because it's the game that completely stomped me. With the other games I haven't completed, it's because I took a break. Here it's because I got stuck and just couldn't figure out what to do next. I hope to rectify that when the 3DS version comes out, but until then I consider it the most difficult out of the 3D titles.