I think it really depends on how you approach your app.
For example, Basecamp uses domains because each space is on its own, without sharing nor communicating with others. Thus, conceptually, you could approach subdomains as different, parallel versions of a simple concept (a business account, a work project, etc).
On the other hand, folders, all nested on the same root domain, seems more a part of something
than something on its own.
Since they are teams who, on some way or another, share info, comments and stuff like that, I'd say the second approach feels better. And it's technically more easies to accomplish.
At the end of the day, both could be use to be the same, but some patterns (like I've commented before) tend to be use on one or other situation. It really depends on your take :)