According to this article in Current Science, Episodes, a geosciences journal, has the highest impact factor as per the SCIE (Science Citation Index Expanded) – 3.263. The article’s source is the Journal Citations Report 2016 which I can’t access and independently confirm.
Episodes was published by the International Union of Geological Sciences along with the Geological Survey of India (GSI) until December 2016. From 2017, it will be run by the Geological Survey of Korea.
GSI has its own journal, Journal of the Geological Society of India, but as per wikipedia, it only has an impact factor of 0.424 (citation needed). The two journals also seem to have had the same editor, Fareeduddin.