Spider-Man hasn't always had the best track record with Marvel's other heroes. Peter Parker himself has some good friends, but most of them aren't capable of keeping up with Spider-Man. The Human Torch, however, knows both Spider-Man and Peter Parker, making him the Web-Slinger's best friend.
Of course, this friendship started off more like a friendly rivalry. In the Amazing Spider-Man #1, by Stan Lee and Steve Ditko, Peter met Johnny Storm for the first time when he broke into the Baxter Building. The resulting fight didn't necessarily put the two heroes on the best of terms. From this point forward, Spider-Man and The Human Torch were very competitive with each other, fostering a healthy young rivalry.
Eventually, however, a bond grew between the two. In Strange Tales Annual #2, by Lee and Jack Kirby, Peter and Johnny had their first major team-up to take down The Fox. Obviously, Spider-Man and The Human Torch fought at first, but they soon came to respect each other's abilities and have teamed up fairly often since then.
Johnny even became a source of inspiration for Peter on occasion. In the Amazing Spider-Man #3, by Lee and Ditko, The Human Torch gave a speech at Peter's high school after Spider-Man was beaten by Doctor Octopus. Hearing Johnny speak, Spider-Man was inspired to get back in the game and defeat his foe. The fact that Peter and Johnny were both teenagers allowed them to relate to each other more than anyone else. Untold Tales of Spider-Man #13, by Kurt Busiek and Pat Oliffe, for example, revealed how Peter confided in Johnny after Sally Avril's tragic death.
These smaller moments between Spider-Man and The Human Torch helped them become much closer. It says a lot that the first issue of Marvel Team-Up, by Roy Thomas and Ross Andru, paired Spider-Man with The Human Torch. Shortly afterward, Johnny helped Peter create the infamous Spider-Mobile in the Amazing Spider-Man #130, by Gerry Conway and Andru.
The process of creating this Spider-Mobile was revealed to have brought Peter and Johnny closer together in Spider-Man/Human Torch #3, by Dan Slott and Ty Templeton. During their time working together, Peter told Johnny all about Gwen Stacy's death and the guilt he harbored. Johnny sympathized, but he also helped Spider-Man get back on his feet, using the Spider-Mobile to help Peter have fun again.
The whole Spider-Man/Human Torch mini-series encapsulated the strong bond between Peter and Johnny. The two heroes practically grew up together, making Spider-Man and The Human Torch akin to brothers. Peter and Johnny would fight and pull pranks at the other's expense, but they grew all the closer for it. In Spider-Man/Human Torch #5, by Slott and Templeton, Peter unmasked himself to Johnny, showing how much he trusts The Human Torch. Moreover, Peter and Johnny both admitted that they were each jealous of the other, each hero wishing he had the other's life.
Even after "One More Day," when Spider-Man's secret identity was wiped from the public consciousness, Peter unmasked for Johnny and the rest of the Fantastic Four in Amazing Spider-Man #591, by Dan Slott, Barry Kitson and Dale Eaglesham. This move demonstrated how close Peter was with Johnny and the rest of the FF.
In FF #1, by Jonathan Hickman and Steve Epting, Peter took Johnny's spot in Marvel's First Family while Johnny was presumed dead. Joining the FF cemented Peter's place as Johnny's surrogate brother. Even after The Human Torch returned, Spider-Man stuck with the FF for a while.
It's true that Spider-Man is pretty close with other heroes, like Daredevil. Peter and Matt Murdock certainly connect as two street-level heroes who have endured plenty of hardship. Still, Matt doesn't share the connection of age that Johnny does with Peter. Both Peter and Johnny are also fairly goofy, cracking jokes quite often. Daredevil will do this on occasion, but not to the extent of Spider-Man or The Human Torch.
Peter also has plenty of ordinary supporting cast members who could be considered his best friend, like Harry Osborn or Mary Jane. Yet Harry has proven mentally unstable, turning into a villain on several occasions. Mary Jane might rank slightly above Johnny, as she is privy to both aspects of Peter's life and knows him better than almost anyone.
Even so, Peter's life as Spider-Man has proven a great burden for Mary Jane on occasion, since she's not a superhero. The Human Torch, on the other hand, understands the superhero lifestyle, living through some of the same wild events as Spider-Man. Johnny may not share the level of intimacy with Peter that MJ does, but he can share the experience of being a superhero. This shared experience allows The Human Torch to relate to Spider-Man in a way even Mary Jane can't.