iPerf or Tamosoft throughput test. As a primarily Mac shop I currently find TTT more convenient, as iPerf builds for Mac are somewhat limited to specific OS versions or "build it yourself". TTT is a straightforward (and cross-platform) download and run.
...but iPerf is by far the more commonly/widely accepted method among network professionals.
Have used both, not affiliated with either. The old "copy a large file from a computer here to a computer there" method is also informative and straightforward.
To the horror of cable salespeople, you will probably not find any noticeable difference between Cat5e and Cat6 segments, unless a segment of either type is kinked or otherwise defective...Or plugged into a non-gigabit switch...