After having looked at each of these two projects, it seems that both are VERY similar. Both run on top of the CLI, both have python style syntax, both use .NET instead of the standard python libraries.
So, what are the differences between them and advantages of each?
I have written applications in both Boo and IronPython.  For me IronPython has been the more robust choice and much of what I've written in CPython ports without changes.  All recent projects have been pure IronPython if targeted for .Net Framework.
Since Jim "defected" to Microsoft, IronPython has been elevated to a top tier language.  There's even Visual Studio for it.
Boo vs. IronPython