i know inventor 09 has some nice features but i dont know if they have any thermo properties yet. I have done thermal analysis before in unigraphics nx4 and nx5 but these are not autodesk softwares.
you cold try something separate from cad like radtherm
there is a 30day free trial so you can play around with imports/exports.
there are several stand alones out there so im sure one would work but i dont have any experience with them, sorry.