Very interesting that you chose to exclude Zelda II: Adventure of Link as well as Majora's Mask. We'll be sure to see quite some diversity in terms of replies in this thread.
With those two choices aside, I thought the hardest Zelda game is A Link to the Past. Starting from as early as the third dungeon, The Tower of Hera, the difficulty level spikes significantly upward. After obtaining the Master Sword and travelling to the Dark World, however, things start to get very interesting. The overworld is filled with baddies around every nook and cranny. The dungeons are also very well designed with many secrets hidden in destructible walls as well as a confusing layout which truly requires the player to bust out the dungeon map. Bosses in 2D Zelda games may seem like a piece of cake with only a length and width plane to navigate but that could not be farther from the truth. Something the bosses in ALttP do a lot is move. In this respect, they are a lot harder than those in modern 3D titles who are stunned upon impact giving you time to slash away/ A Link to the Past truly is a masterpiece, however, to me it is something much more-A painful lesson in how hard games were during the golden era of 2D gaming.