Depends.
What is your budget, and what do you plan to take macros of?
I do insect macros, so I chose the excellent sigma 150mm over the (also excellent) canon 100mm for the extra working distance. They are to all practical purposes, equal in IQ, the 100 has slightly faster AF which is a bit less prone to 'hunting', but I never have any problem with the AF on my 150 in good light, especially considering I always manual focus for macro anyway.
For things that fly away, extra working distance is valuable, but it doesn't really matter for stationary things like flowers.
One thing that doesn't seem to often get mentioned is that longer lenses will give a more diffuse background at the same aperture, which can make for more pleasing photos of things like flowers.