It is laughable to think that India has the wherewithal or skill to carry out an assassination across the globe. You need to have the infrastructure and more importantly, the support of your western allies if/when things go sideways. As others have pointed out, there are more prominent Khalistani/Tamil/Kashmiri separatists that India wants to target but they are either unable to or don't want to. India does target them in South Asia but I doubt it can do it in Canada.
What most likely happened is this. Nijjar had already been involved in petty crimes and gangland violence in Canada. He was probably killed by a rival gang. One only needs to google this. It's election season and Trudeau wants to appease Jagmeet Singh of the New Democratic Party that is keeping him afloat. Also, 4% of the Canadian population is made up of Indians, most of whom are Sikhs.