Near as I've ever been able to determine he wasn't. The charge is usually made because the crown and cross symbol he used is also used by the Masons. But, then, it was also used by other groups as well, so that in and of itself doesn't prove he was connected with them. I seem to remember the subject coming up on another forum somewhere and a Bible Student posted a quote from CTR in which he denied any invovlement with the Masons.
I've also seen the fact that a Masonic temple now sits on land near CTR's grave used as proof that he was a Mason. However, that temple was built only a few years ago on land that it appears was sold to them by it's former owners, the WTBTS.