Rinnegan > EMS to me this seems to have been made relatively clear in the manga...That is why the evolution of sharingan eyes final stage is the rinnegan. 2tamoe < 3tamoe < Mangekyo < Eternal Mangekyo < Rinnegan
Of course the most powerful dojutsu possible would be a user who could use EMS before they unlocked the Rinnegan since they will have access to all EMS and Rinnegan techs, rather than a person who just transplanted Rinnegan into their eyes. I.E. Madara has more powerful dojutsu techniques than Nagato because he has access to all rinnegan techs AND his EMS techniques.
It is unclear whether it's possible for someone to use EMS techniques having transplanted a rinnegan, since Nagato didn't seem able to do so. Yet, Madara has used EMS techniques with the Rinnegan active, which makes it unclear to me.
In my opinion, comparing the two, the Rinnegan has more powerful and a wider range of useful techniques than does an Eternal Mangekyo Sharingan, though I'd say they are at least close and the decider of a battle would be who has better use of their eyes rather than who has more powerful eyes.