Definitely Naruto and Kurama are at the top. Their connection was central to the Naruto story. But Naruto and Shukaku, the One - Tailed Beast, also make for an interesting pairing in fanfiction. Shukaku's grumpy and sarcastic nature contrasts well with Naruto's optimistic and determined self. And then there's Naruto and Matatabi, the Two - Tailed Beast. Since Matatabi is more of a calm and collected entity compared to some of the others, it creates an interesting dynamic when paired with Naruto.
Naruto and the Nine - Tails (Kurama) are probably the most popular. Their relationship throughout the original series was so complex and full of development that it's a natural choice for fanfiction. Also, Naruto with Son Goku, the Four - Tailed Beast, has some popularity as they both have strong - willed and somewhat hot - tempered personalities which can lead to interesting interactions in fan - created stories.