Neither is easy to measure. However, my intuition is that capabilities, in the sense that Nussbaum and Sen use the term, are broader than well-being. The question of whether we have the freedom to realize our possibilities is captured by the notion of capabilities. 

Moreover, as a criterion for non-human lives, capabilities may also work better: we can assign specific capabilities to different species as our criteria. With that approach we may debate whether a long life is something we, as humans, should wish for a bug, while still recognizing its bodily health and bodily integrity.