Either one can be made to work, they will just get the job done differently. I personally feel the advantage goes to the smaller CID in a limited compressor application, but be prepared to really work hard on getting the rest of the combo happy. The advantage to the larger CID is in torque production at a lower rpm, which will make it easier to drive. In most cases it will lack the power curve to take advantage of the converter/gear/camshaft needed to exploit the most out of that turbo size.
Good luck!