As far as I know the this Taj Mahal as Shiva temple theory was propagated by a self taught, self proclaimed historian P N Oak. I am not discarding his theory because he did not have proper training but his evidence and logic does seem to be pretty shaky.
I will not go into specific details on this answer but Indologist Dr. Koenraad Elst has deconstructed all his arguments here.
Salient points for the record:
- Textbooks of Hindu temple building are pretty well written. None of them would recognize Taj Mahal as a temple.
- The very fact that a lot of the actual builders and masons employed could have been Hindu, their influence on finer details is to be expected but that does not make the whol building Hindu.
At any rate, even if standing on a Hindu site, the Taj Mahal is absolutely no Hindu building. It entirely follows the conventions of Indo-Saracenic architecture, with domes and arches borrowed by the first Muslims in West-Asia from the Byzantines, with no Hindu connection in sight anywhere. As a grave, too, it is wildly contrary to Hindu sensibilities. Only accomplished (jivanmukta) sages are buried, other human bodies are cremated or, in related (Parsi, Tibetan) traditions, left to disintegrate under the impact of animals and the elements. The idea of keeping decomposing human bodies close to human centres of habitation in graveyards is repulsive to the Hindu mind. It is a sign of Hindus’ estrangements from their roots that they insist on claiming this un-Hindu site, probably because (Brahmachari writes as much) it is applauded world-wide. Well, proud Hindus don’t care for the poor taste of Western tourists and may point out that the Taj Mahal is bland and vulgar when compared with Ajanta and Ellora, the Meenakshi temple or the Elephanta caves.
In defence of his thesis, Brahmachari challenges the sceptics to explain one particular inscription dedicating an unspecified marble temple in the area to Vishnu. It is not clear from the inscription as given by him that one of the temples stood at the very site of the Taj Mahal. According to his own data, at any rate, the inscription is from ca. 1150 AD. That is well before the destruction of just about every temple in North India by Ghori and Aibak in 1192-94 and by their successors in the Delhi Sultanate. Especially in Agra, lying on the main route of Muslim advance and a sometime Muslim capital, no sizable temple could have been left standing in that orgy of iconoclasm. So there is some 500 years between the destruction of the said marble temples and the appearance of the Taj Mahal.