I'd want to take it off just to avoid all the metal shavings from getting down into the mechanism and all over the top. And knowing me I'd drill a hole through my top.
You'll have to drill the hole out slightly oversized (assuming there's enough material to do so), then tap it (causing more shavings), then insert the repair coil. All those steps should be done as straight as you can, which is probably going to be a lot easier off the car than on.
With all that being said, it's up to you. Nothing says you *can't* do it while the top is on the car. Does putting the top partially up give you any better access? BTW, do you still have the washer that goes between the lever and the bow?