This may be less helpful than you want, but it will really depend on what you want to measure. And maybe the Reynolds number as well. If you just want to see that vortex shedding is occurring and measure frequencies, you could measure quite far from the centerline. And you probably want to be a few diameters downstream, but you can go much further away. From the excellent video here: www.youtube.com/watch?v=_AJgEa2dbJU you can see how far the vortices extend.
I should add that you can't place your probe at y=0 because it touches the wall and will burn. So start from somewhere away from the surface and bu extrapolation methods you find the surface condition.
I use flow visualization to place the hot film/wire probes in the vortex street in order to determine the vortex shedding frequency of cylinders. In several flows, the velocity Fourier Transform shows very difficulties in order to determine the fundamental vortex frequency, principaly to very low frequencies. Flow visualization is a useful tool in order to place the probes and to obtain a good relation signal to noise in the FFT. Please, see my papers to more details.