Copying a large file from an USB 3 disk (NTFS or EXT4) to another one (UFS/FreeBSD) is a very slow process

I posit the problem is using rsync - its likely doing a lot of reads to work out its position and only send diffs - ie its not the correct tool for the job.

You may be able to solve this using (gnu) ddrescue - this makes a "status" file allowing you to resume broken copies. Its designed for moving block devices but should work just fine here as well - provided the disk image does not change while being copied.