I think that the only Prime Minister who can be called genius to some extent was Mr Narsimha Rao.
He is often referred to as the "Father of Indian Economic Reforms".
He was perhaps the only PM who showed guts to appoint a non political person, Mr Manmohan Singh, as the Finance Minister and gave him free hand to bring economic reforms in India that actually has created the modern India.
He also appointed an economist, Mr Montek Singh Ahluwalia, as the Finance Secretary in the Finance Ministry instead of an IAS officer, who usually lead every ministry in the Government of India.
He implemented the boldest economic reforms in the history of India and transformed the nation.
We joined IRS during that time (1991) and I still remember that almost everyone was criticizing the liberalization and globalization policies of Mr Rao and predicted his failure.
However, he has proven all his critics wrong by successfully implementing the policies.
All future governments continued the economic reform policies pioneered by Rao's government.
He was a versatile personality with interests in a variety of subjects (other than politics) such as literature and computer software (including computer programming).
He also spoke 17 languages.
He was also the only PM in India who could run a minority government for full five years.
He was the only genius Indian PM, if any.
References: https://en.wikipedia.org/wiki/P._V._Narasimha_Rao