whois.domain.com doesn't work for me, so I don't know what that is?
Alexa uses "ranking" information that they get from Alexa users that have the Alexa toolbar installed.
I don't know where whois.domain.com gets there information, but any site that provides ranking information only has part of the information, so none of them are very accurate. It can be better than nothing, but if you install the Alexa toolbar and then visit your site everyday, you can see your ranking move up in a couple of weeks.
Those kind of tools can only give you a rough indication of your standing on the world wide web. If you try a few different tools, you can improve the reliability of the information you get. However, it's never going to be truly accurate.
Try websitegrader.com to get a good idea of how your site is getting on.
alexa is a good basis but it is also wise to check others too because as everybody had already said, alexa measures traffic only from people who have the alexa toolbar. You can use alexa as a good reference point but don't forget to take into consideration the others.