I have not seen a published comparison. Perhaps Gartner Group has one, but I do not subscribe.
In a nutshell, Clarity is ideal for many IT shops and it is very expensive ($100K USD and up). MS Project Server is more general purpose, but it is also not as capable. MS Project Server can be customized tremendously, and it can be added onto using MS Project Portfolio Server, Share Point, and their scripting languages. The budget for an MS Project Server roll out can be much less than a Clarity roll out, but if you invest in a lot of customization it can be EXTREMELY expensive.
If you talk to sales reps for either product, they will give you lots of information. They are very accustomed to selling against each other. Saving Changes...
I would like to find a place to discuss usage of Clarity PPM from CA (formerly Niku) - I just implemented the package and would benefit from a user group, if you know where there is one. Thanks Saving Changes...
I would contact my CA representative. Sometimes CA has user groups for its products. Hopefully they will know of any active user communities.
You could also create a community right here on Gantthead. Everyone here seems to be anxious to help members start interest groups right now. I bet they would provide you with great support. Saving Changes...