I think that the question has not been asked properly. The fact that you're smart, doesn't mean that you can not be popular. You can have a high a high IQ, and still have good social skills, and charisma.
Anyways, I choose being smart, because (based in the idea that you can be either smart or popular, but not both), as csuti said, popularity doesn't last long. While being smart will last my whole life (or a least most of it), and I'll be able to make good use of it (at least of good use for me).
Yes, it my feel good being popular (as long as it is because of your personality, or because people admires you, not because people wants something from you, like in the case of you being rich), but unless your trying to base your life in something like the movies, music, modeling, etc... In those cases, you must be talented, but being popular is certainly a good factor of success. Outside those cases, popularity won't really help you much in life.
Not being popular doesn't mean that you don't have friends, or that you won't be able to find a good partner to share your life with. Not being popular just means that you are not one of the (or THE) centre(s) of the attention.