Everyone is talking about Daredevil and Spider-Man and while I will read anything with the two of them in it (loved Waid's take on their friendship); the best friendship for Matt (and maybe in all of Marvel) is his friendship with Foggy Nelson:

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They have been best friends since Daredevil #1 and have gone through so much during their friendship.

Even if we are talking those in the superhero community, I would say that Matt has a deeper friendship with Natasha than Peter and it's not just due to the fact that they dated. They have stayed close and have been there for one another when they needed it.