The radix-3 is related to the total length of the FFT (the length is a power of 3, e.g., 9,27,81) not the type of data you are transforming. The length of the data buffer will not be a power of two which means some wasted addressing and the possiblity that the inherent RAM sizes will not be fully utilized but who cares? Memory is cheap in FPGAs nowadays.
I think you can apply the standard Cooley-Tukey implementation which gives a good solution for size 2^n, 4^n, 8^n etc. which I have used for radix-2, radix-4, and radix-8 as well as mixed radix FFTs but never for 3^n- sized ones.
I googled and got some hits for "radix 3 FFT" so I know there are reasons to use it.