Maybe through SSH or FTP
What kind processes are you running?
If you just downloaded Nicaw and didn't edit nothing, it's fact that the hacker use some vunerabilities of Nicaw like uploading exploits and get access to your computer.
Nicaw have serious vunerabilities.
Why don't you use a program to check out your vulnerabilities in your website?
Try Acunetix.What program?
Try Acunetix.
You can get the crack.It only scans for cross site scripting, unless you pay for the program.