Unfortunately that is largely what we have to go off with the NSA.
It's another layer entirely and does not give information about their capabilities in attacking tor itself (except maybe through the fact that if they had to do that, then yeah, tor is probably still relatively secure if used properly).
You're right; actually tor reside in the application layer I think (above TLS).
Although conceptually speaking it is itself a transport layer I guess.
Layer 5 would be HTTP, layer 6 would be the content (JPEG, MP4, etc.), and layer 7 would be the application serving or sending the HTTP requests/content.
Fortunately Internet wide timing attacks are mostly a Five Eyes and domestic Chinese capability. Chaff, padding etc can help here.
Compromising the servers of target services and using that a platform to distribute anonymity stripping malware is also a problem. The Firefox codebase that TBB is based isn't awesome from a security point of view. Hopefully the Firefox code base can catch up from a security perspective and give them something better to work with.
There's even users who configure BitTorrent to use TCP instead of UDP so that it's very difficult to write DPI rules to parse out the TOR traffic. Couple this with meek, VPNs and traffic shaping tools and it's quite bothersome for them.