I'd first try to find out if your networking (inside cygwin) is slow. You could try to use iperf to run some basic benchmarks.
On the server:
iperf -s
On the client:
iperf -c <host of server>
This should give output showing close to 100 MBit/sec. If not, the problem is unrelated to rsync (and the encryption you use because of the SSH access).