Rake and Thor serve different purposes.
Rake is a general build script tool that is project-specific. In other words, you put your rakefile your project folder and in your project's source control, and you create build and other automation tasks that are specific to your project in that rakefile. rake requires a rakefile to run.
Thor is a general purpose command line scripting tool that makes it very easy to re-use scripts across many projects and to do project setup, etc. like you are suggesting. Thor allows you to "install" an executable script that you can call from anywhere on your system, similar to calling "ruby", "gem" or "rake" command lines. However, thor's scripts are more suited to general purpose, cross-application automation because the thor script does not rely on a file sitting in your project specific folder. a Thor script is the entire script, packed and installed for re-use anywhere.
Based on your stated needs, you are better off using Thor because you will be able to install your script in one location and have it work anywhere on your system. you will not be bound to a rakefile sitting or anything like that.
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by the way: Rails 3 uses Thor for pretty much everything that is not project specific. you still have a rakefile and you still run things like "rake db:migrate" or "rake test:units". Thor is used for things like "rails new ...", "rails server" and "rails generate ..." The use of Thor AND Rake in rails 3 is the perfect illustration of where each of these tools is best suited.