Actually, the most recent revision of the Dangerous Goods regulations that govern shipping things by air drops the requirement that you need to disconnect the motorcycle battery. The key criteria is whether or not the battery is 'sufficiently protected' within the vehicle, which in the case of just about all production motorcycles, it is.
It takes quite a while for this kind of information to percolate down through the ranks to the folks who are accepting the shipments, so, you might still get asked to disconnect the battery. In principle, though, all you have to do is just show up with less than a quarter of a tank of gas and voilà, that's all.
The company accepting the motorcycle for transport will need to complete a checklist to ensure everything has been done right. Part of the checklist includes checking to see that the fuel tank is 1/4 full or less. If you have a locking fuel tank, it is a good idea to leave it unlocked (depending on the model of bike, this might mean removing the lock from the flap, or attaching a key to the gas flap with a tie-wrap).
A very important consideration when shipping to Canada is that the motorcycle must be very, very clean and free of dirt or insects. This means taking a high-pressure hose to the underside of the fenders, wheel wells, etc. and removing all dirt and mud. Otherwise, the Canadian Customs folks might want to call an agricultural inspector to come and have a look (to make sure that no invasive species, etc. are being imported with the dirt, or with the bugs on the windscreen), and this agricultural inspection will delay release of your motorcycle by a day (running up your storage charges) and will also result in a $100+ fee for the agricultural inspector. So... to avoid headaches, ship it clean!