McCann's knock came unstuck on 92, with Cameron Neal unbeaten on 45 when the innings came to a close at 279.
Hamilton bowler Clint Price was rewarded for plenty of honest toil with figures of 5/60.
Hamilton resumed at 16 without loss on day two, with the match continuing to hang in the balance for much of the afternoon.
The key Hamilton wickets of Peter Bocock and Anton Devcich tipped the contest in the Bay's favour, with Hamilton falling from 218/7 to be removed for 235.
Brett Hampton took a five wicket bag, while Campbell Thomas and Jono Boult took two wickets apiece.
The result means the Bay has taken the early lead in the year-long race for the Northern Districts right of challenge for the Hawke Cup early next year.
Fergus Hickey Rosebowl, Bay Oval, Mount Maunganui: Bay of Plenty 279 (M McCann 92, T MacRury 53; C Price 5/60) defeated Hamilton 235 (P Bocock 33, A Devcich 31; B Hampton 5/56, Campbell T 2/31, J Boult 2/67).