You can recruit all the generals you want and natives have low morale, so if you use a bunch of bodyguards to charge en masse into their flank I bet you could rout quite a few of them. While I wouldn't suggest going with more than 3-4 bodyguard units, it's obviously a high cost strategy.
You might also want to consider selling it to say, France for Martinique or to Spain for one of their 8 territories outside Spain proper (Gibraltar being your best bet). You might even be able to trade it for Corsica to Genoa or Denmark for Iceland (to get a couple warship factories). Whatever you sell it for, it will likely not be a wealthy territory by any standards.
Either way, I'm sure it will repay you later on if you can keep Moose Factory or even sell it for a slight downgrade. It's just a huge a pain to send an army up there, by land or by boat, and can end up costing you a lot of money to keep a large garrison in the town. Kind of like Carthage's territory in Sardinia in Rome:TW. It's worth selling to Greece or Spain to get Rome to go to war with them and leave you alone - at least for a little longer.
Then again... Rome was a lot more powerful than a bunch of native americans with bows, arrows, and tomahawks.