If you are just interested in the rate of precession, then $r$ just has to be the distance from the support (tip of the top) to the center of mass - this is the distance that gives rise to the torque through $mgr\sin\phi$
However, if you want to do this as a vector equation, then you have the instantaneous angular momentum (vector) of the top $I\vec\omega$ which points along the axis of the top, and the torque vector which is at right angles to this (namely, $\vec {r}\times\vec F_g$ - possibly with the sign flipped...)
I think for your purpose, if you assume that the rate of precession is constant you don't need to delve down into the details of the vector math / calculus - you will get the right answer just using the distance to the COM and applying the correct value of $\phi$. Do pay attention to the direction of the precession (from the link, you can see it is in the same direction that the top is spinning - so looking from above, if the top spins clockwise, then it also precesses clockwise).