During Hurricane Irene, we had water permeate the mortar in our glass block bathroom window. What do we do to make sure it doesn't happen again?

Silicone spray, then wipe it all off the glass.
For even more protection, clear silicone adhesive from a tube first, working it into the mortar and wiping it down. It needs to be totally dry in either case, and not to cold out.

That or chimney sealer. Something designed to seal masonary. ChimneySaver Water Repellent brick sealer for brick waterproofing, chimney waterproofing and leaking chimneys (http://www.fireplaceandchimneysupply.com/ChimneySaver-Water-Repellent-WB-p/ss_csw.htm) Hopefully you can get in in a smaller container than 3-5 gallons.

Grout sealer will also work. Brush it on with 2-3 coats.

I would think that your problem is from poor window flashing, not leaky mortar. Are you absolutely sure its coming from the mortar lines?