Does anyone know who or what sect has taught or teaches about the amala-vijnana ("stainless" consciousness?)
As far as I know there was only one individual who taught this; an Indian by the name of Paramartha (499-569.) Also apparently the Nichiren sect teaches this, according to this website I found while doing an internet search of the subject: http://www.sgi.org/buddhism/buddhist-concepts/the-nine-consciousnesses.html
Is that a legitimate source for what the Nichiren sect teaches? Because I thought it was based off the Lotus sutra and from reading the Lotus sutra: I didn't see any mention of an amala-vijnana?
First of all, this consciousness as it has always been present in Buddhism and was taught by Lord Gautama. It is the nibbana consciousness, pure, endless, and luminous all around.
Furthermore, as Malcolm implied, I doubt that anyone has legitimately taught it as being the "ninth consciousness." In the eight-consciousness scheme, it is held to be equal to the eighth consciousness. That is to say, the storehouse consciousness is simply derived from the substratum consciousness, from which nibbana is also cognizable.
The six sense consciousness plus perceptual consciousness (manas) are amalgamated by the substratum consciousness, and they are derived from it via the presence of the storehouse consciousness (eighth).
To put it into context of understanding, in dependent origination you might say that from ignorance arises intention, from which arises consciousness--storehouse consciousness, manas consciousness. From that arises name and form, and the sense bases (ergo the six sense consciousnesses emerge), giving rise to contact. So, in my mind, consciousness is depicted as contact-consciousnessnes, perceptual consciousness which gathers defilement, and substratum consciousness which includes storehouse consciousness.
Is that helpful at all? I always find putting teachings into context of dependent origination and/or aggregates illuminates them, especially under meditative practice.