Waterproof paint for rubber

You'll need something that's highly durable and flexible, but won't decrease the performance of your fins too much.

It seems you're best off with a rubber(izing) paint or rubber coating/liquid rubber, which is "heat, chemical, weather, and impact resistant, as well as being flexible". Last but not least, according to the linked page, since they are "water based and VOC free, these products will not harm you or the water table".
They are a little hard to find as coloured paints, though.

Be sure to test your coating or paint on (similar) rubber before applying it to your fins, and to clean the fins (using water and soap) for improved adherence (I suppose sanding the rubber is out of the question).

You can read through this thread on scubaboard.com, as it has a few good tips and alternative approaches, or this thread on whitearmor.net (a site aimed at stormtrooper cosplay enthousiasts), where they talk about painting rubber boots.
Looking into cosplay forums can generally provide good alternative ideas.

I suggest using your favourite search engine to look for a proper product if the ones mentioned on the linked websites or in the linked threads aren't to your liking.
A good candidate might be Plasti-Dip, as it is available in multiple colours, but I'm not sure if the peelable nature of it means it will slowly peel off of its own accord. Fusion All-in-one from Krylon also seems to work.

Alternatively, you can use stencils to decorate your fins using the permanent markers.