Solved my own issue.
I was reading a few other post on here and found one that talks about the nsclient.log file located on the Windows server. I looked at it and found "ERROR: Counter not found: \MSExchange\Current Unique Users: The specified performance object was not found on the computer."
After checking the counter in Windows perfom, I found the counter is MSExhcnage OWA\Current Unique Users. I changed the command to
check_command check_nt!COUNTER! -l "\MSExchange OWA\Current Unique Users","%.f users logged onto OWA" -w 1 -c 100
Now it is working fine. It reports the correct number of users logged onto OWA.
Lesson learned... Always double check your spelling.