After South East Melbourne folded, Mackinnon was signed by the Townsville Crocodiles at the beginning of the 1999 season, and it was not long before Townsville became serious title contenders. In 2001, Townsville made the Grand Final, however Mackinnon missed the series due to injury. Once his contract ended in Townsville, Mackinnon elected to sign with the West Sydney Razorbacks where he became their captain and put up career-best numbers in his first season. During the following season Mackinnon led West Sydney into the NBL Grand Final series against cross-town rivals the Sydney Kings. Sydney won the series 3–2.