The boats operated in teams
They didn't go out alone. Those men may not have been on the same boat, but they were out on the same missions at the same time, often only yards apart. They served together, just as fighter pilots in the same squadron and the same wing serve together even if they aren't in the same plane. They most definitely did serve with John Kerry.
The closest thing in my military experience that compares is service in an infantry unit. We had our squads, and the squads were grouped into companies. The companies were grouped into battalions and so on. If we went out on an exercise (my service was during peacetime), we went out in groups. If my squad was out on a patrol alongside other squads, then we were serving together.