that is a bit easier.
Military ships are almost never bigger than 50,000 tons, for starters
Also, there's rarely a reason to have more than 3-4 30,000 ton ships
So if you're seeing lots of aship that's big, it's almost certainly civilian.
The most important hint though is activiity. Think about what your system would look like to an alien: clusters of military ships around planets and jump points, civilian ships constantly flitting through the central system. If you're seeing many copies of a big ship that's moving around a lot with other ones like it, it's almost certainly a commercial ship, possibly a jump point constructor.