The best way to hunt shiny Pokemon in the ultra-warp ride is to always aim for the Type-4 Portal, which is the portal with the largest ring around it (In other words, it's the portal that will look the largest). Keep in mind, the colour of the portal will not have any effect on shiny encountering. The colour only determines what Pokemon you have a possibly of finding a shiny of.
Not only the size (type) of portal, but the light-years traveled also has a large influence to the probability of finding a shiny Pokemon. All the information about types of wormholes and shiny calculations ca be found here, but you can tell that a Type-4 portal with the furthest amount of light years traveled will result into the highest probability of a encountering a shiny Pokemon (being approximately 36%).
Hope I helped! :)