In Fallout 4, one of the best companion stories is probably Piper's. She is a journalist with a strong sense of justice. Her story involves uncovering secrets in the Commonwealth and fighting for the truth. Another great one is Nick Valentine's. Being a synth detective, his past is full of mystery and his journey of self - discovery while helping the Sole Survivor is really engaging.
One of the best companion stories is that of Dogmeat. He is a loyal and loving companion from the start. His story is simple yet heartwarming as he's always there by your side, ready to help in combat or just be a furry friend during your exploration in the wasteland.
Piper is a great choice for the story. She's a journalist with a curious nature. She'll often comment on the events in the story, adding some interesting perspectives. And her personal quest also ties in well with the overall narrative of Fallout 4.
Dogmeat. He's the most loyal and always there for you. He doesn't have complex dialogues like some human companions, but his presence is reassuring. He can also help you in combat and find things for you, which is really useful during the main story.
Piper is a great companion for the main story. She's a journalist so she has an inquisitive nature. She often comments on the events of the main story in an interesting way, which adds depth to the overall experience.
I think it's Hancock. He's a ghoul mayor with a wild past. He used to be a chem addict and has done some dark things. But he's now trying to make things right in Goodneighbor. His story of redemption and his unique view on life in the wasteland are really captivating.
Deacon is really good too. He's a bit of a mystery man, and as you progress through the story, you start to uncover more about him. His skills are very useful in the story quests, especially when it comes to stealth and infiltration. He also has a great sense of humor that lightens the mood during the often - dark story of Fallout 4.
Lily Bowen can also be considered a top companion for the story. She's a Nightkin with a unique personality. Her relationship with the Courier can be quite endearing, and her story arcs, especially related to her past and her 'granddaughter', are very engaging and add a lot to the overall narrative.
The different scenarios. Fanfiction writers can create all kinds of new situations for the companions. They can take Hancock to places he's never been in the game's main story, and show how he reacts. It adds a whole new layer of depth to the Fallout 4 universe.
One of the best companion stories in FNV is probably Boone's. His backstory of being a former NCR sniper and his quest related to his wife's death is really engaging. It adds depth to his character and the overall lore of the game.