I would say The Great Deku Tree. I actually had some trouble understanding that I had to jump and break the spiders web when I first played it as a child(very young). But yeah, thats for sure the easier both in dungeon and boss.
OoT was my first Zelda game (and obviously the first 3D one for anyone playing them in order of release) so I probably took longer to complete the Deku tree than Dodongo's cavern first time around because I was just getting to grips with a totally new control. But looking from a totally objective stand point, Deku tree is by far the easiest of the 3.
Inside the Deku Tree for SURE! I took me about 4 minutes to finish the dungeon and about 25 seconds to defeat the dungeon boss.. I had absolutely no confusion the entire time. It was so short, I didn't even know it was a dungeon..
It's hard to answer this question having now beat the game and kowing each dungeon inside out. I personally believe it was Inside the Deku Tree although I did get stuck with trying to break the spider web to descend when I was younger. Also, none of the puzzles were particularly perplexing-shooting eye doors with your slingshot, moving blocks, and reflecting Deku Scrubs' shots in a particular order. The boss battle was quite perplexing for me the first time around, however, it is a joke now especially seeing quick speed runs of it on the Internet. I do believe King Dodongo is a tab easier though.