The short answer is no, because to access (and this convert) proprietary Thermo raw data, you need to their libraries that are only available on Windows. That would mean that an R package would need to (i) incorporate these proprietary binary Thermo libraries and (ii) only be available on Windows.
You will need to use msconvert from the Proteowizard project (on Windows) to convert them to an open format such as mzML or mgf. The latter can be processed in R with MSnbase.
It is apparently possible (although I have never tried it myself) to get the Thermo libraries to run under Mono on Linux. I don't know if this would also work on OSX though.