So the highest chance of getting a shiny from of chaining is 1/200, which will happen once you get to the 40th Pokemon in your chain. After that, the chances of getting a shiny are the same.
Masuda Method gets the chances of a shiny to 1/1365, so on the surface of things chaining is quicker.
However, shiny chaining requires a lot of concentration and effort, not just time. Masuda Method really only needs time, since all you need to do is cycle around to hatch eggs. It also takes a significant amount of time to get proficient at shiny chaining, since the chain can break pretty easily.