It feels as if they were.
We never saw Bobby until IMToD, but Sam seemed completely relaxed and familiar with him. And John handed off the list of ingredients forr Bobby to fetch just like they'd always done things like that for each other, like Bobby was ...not a stranger. Like everyone else John seeme to come in contact with.
Plus, there's been a ton of wee!chester and teen!chester fic featuring John and Bobby, so it just seems normal that the two men knew each other for a long time, and well.