All that he means by saying this is that they are really good friends.
Some people say that you can tell that you are good friends with someone when you just know what the other person needs and what they are feeling without talking. That's what's going on here.
Ponyboy says this while they are at the movies and have met Cherry. He is contrasting how he feels around her with how he and Johnny get along. With Cherry, he feels like talking -- it's a different relationship than he has with Johnny.
Ponyboy is saying that he and Johnny instinctually understand each other because they are similar types of people who happen to be really close friends. Ponyboy and Johnny are both young, sensitive boys who are members of the Greaser gang. They come from similar backgrounds and have a lot in common. They are also quiet boys who have sympathy for others. Their sensitive nature and calm demeanor make them stand out from the other members of their gang. The boys also spend a lot of time together and seem to instinctually understand what each other is thinking without speaking. Throughout the novel, Ponyboy and Johnny are supportive of each other and hide together in an abandoned church to avoid police. During their time spent in the abandoned church, the two become extremely close, and Ponyboy gains valuable insight into Johnny's life and personality.
Pony Boy and Johnny are from the same world. In the book "The Outsiders" they are the closest of friends. Both boys are close in age and can relate very well to each other. Johnny is more sensitive than the others and so is Pony Boy. They are the ones who talk about their feelings. There way of life, experiences, and community are so intertwined so that they don't have to say what is going on with one or the other to know how that person is feeling. For example, when Johnny flinches after Two Bit puts his hand on their shoulders at the drive -in movie, Pony Boy knows that Johnny was not just a little startled but was really scared because of always being beat up by his parents and having been jumped and hurt by the Socs.