To reach Knysna from India, you will have to take a flight to Cape Town first and then drive/ take a bus/ take a taxi to Knysna. That being said, there are no direct flights from India to Cape Town. Flights can be taken from all the major international airports and carriers such as South African Airlines, Qatar Airways, Etihad Airways, Ethiopian Airlines etc provide services along these routes.
VFS Global runs South African visa centres in India. Tourist visas can be applied for from the website. The application of the South African visa only requires the logistics fees and is free of visa fees. All the other requirements of applying for the visa can be found at "vfsglobal.com/southafrica/india"
The nearest international airport is Cape Town and there is also a domestic airport in George. Buses or taxis can be taken from there or you can rent a car.
Driving into Knysna is the most preferred way to get here from nearby cities. About 5 hours time from Cape Town along the N2, and around 3 hours from Port Elizabeth from the other side of the N2.
Knysna hasn't has had a railways station since 2006. Major flooding completely destroyed the railways and since then the nearest train station is in George
Within Knysna, the best way to get around is either on foot or by renting a bicycle. To explore the Garden Route you can take the public minibus or rent a cab. However the best way to explore the entire region is renting your own car. Do remember that if you're going during peak season (December to early February), traffic can get fairly annoying.