Thunderbolt bridged with ethernet gives poor performance
The best way to diagnose a network issue is to look at the packets. 


sudo tcpdump -i en0 


You can compare the types of errors and retransmits and high level aspects of the good transfers with the slow transfers. Since the logs are very  might need to save them to a capture file (see the manual page for tcpdump) and use a tool or script to summarize the data.