I am going to nominate Unearthed as the best quest in Dragonborn.

First, I liked how it unfolded over time, rather than just being an in-and-out dungeon dive. I liked reading the journals and seeing Ralis's descent into madness. I also liked how I could see the end boss very early on by using Aura Whisper and knowing that at some point I would end up fighting that guy burried in the depths of the Barrow. By the fourth time I visited the place it was getting a tad tedious, but the pay off worked.

I haven't played the MQ yet, but I liked the find-the-spy quests. I like mysteries and it was fun guessing.

To me my favorite was The Summit of Apocrypha. You can say whatever you want about the questline but the whole proving the strength of your Thu'um to a dragon, riding him to fight Miraak, his dialogue and even the battle itself- win.

even though most of that whole quest is scripted ..yea its pretty fun

I like the finale with Miraak as well, especially if you aren't using OP weapons.

I have only fought Miraak twice. The first time was the hardest since I just landed my dragon and then me and Miraak fought. He kept using Whirlwind Sprint to dodge, making life difficult. The second time I didn't land the dragon: I fought the two other dragons from dragon back and then fought Miraak from dragonback as well. In the end, though, Miraak used that shout that kills dragons and I fell off my dragon and had to fight him normally. BTW< Miraak was rather PO'ed that I was using one of his dragons to fight him.