Generally speaking, deadly force likely to cause bodily harm is not justified to merely defend property.  Typically, deadly force is only justified when the person using it reasonably believes that the intruder is likely to cause death or serious bodily harm to you or a third-person that you are privileged to protect.  Therefore, unless the thief is using deadly force against you to steal your motorcycle, you likely do not have the right to shoot him or her.
The situation may be different if the thief was committing burglary when attempting to steal your motorcycle.  Courts have held that use of deadly force is justified where the facts show that the burglar threatened or was reasonably believed to threaten death or serious bodily harm.

At any rate, you may want to consider other options to protect your property, such as a putting it into a secured garage or perhaps asking your apartment manager whether they are willing to install surveillance equipment.