Let KAYAK do the searching
Based on KAYAK hotel searches, the most popular destination is Little Current (45% of total searches to Manitoulin Island). The next most popular destinations are Gore Bay (25%) and Mindemoya (22%). Searches for hotels in Manitowaning (8%) are also popular.
KAYAK users have found double rooms in Manitoulin Island for as cheap as $95 (Mindemoya) in the last 3 days. The average price is $163.