Tim,
I think James Mark has the right idea - use Bare Metal Foil.
I've used Scotch tape, Humbrol liquid mask, the peel off face mask that ladies use (it works), masking tape and just about every other bloody thing to cover up, but I've never gotten as good results with them as I have with Bare Metal Foil - the stuff is so easy to use and works so very well - I always get great results using the foil.
It's cheap and easy to apply and remove.
I always attach the canopy to the airframe before I paint (unless I model a sliding canopy that's open).
I already answered a question like this in another FSM forum, but if you want, email me and I'll send you a copy of detailed, step by step instructions on how to use the foil to mask canopies or windows.
Or, if you all want, I can just re-post it here - what would you like me to do?
Cheers,
LeeTree