There are arguments that can be made for both.
I believe he was a devoted Mason. When Pike re-wrote the degrees for the Scottish Rite, I read that Pike had taken some of the Degrees from the York Rite degrees and created a controversy by using them.
There are also some of the writings of Pike that are often quoted by Religions such as the Catholics that support the Masons as being a Religion in and of itself. simply the use of Dogma, a term usually associated to doctrines belonging to a religion and the references of Pike as to how Masonry should be followed.
Genius, I'd say so in just the work he entered upon to help bring up the Scottish Rite to a major Masonic Body.