Due to multiple factors, expect to potentially pay more when booking in November. For low rates, May can be a great choice for travel to San Juan. Flights to San Juan from Missoula in May are about $656 on average during May, but can be found for as low as $252.
Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Missoula to San Juan as you normally would.