Depends on if you are lifting it with a couple of guys / gals or using a hoist system?
If you rig a system that supports the roof and does not rely on the roof rack you can leave it on. If you have strong backs and will be storing it on roof sides you can leave it on.
If you are using the rack to pull up on, I suggest removing the rack.
I made my system for the 88 from 2x4 hooks and pulleys. I put a 2x4 through the open rear windows and one up front and would take my top off by myself.
For my new 4 door jeep I use a commercial system that lifts in a very similar way.
Sean
1971 Series IIA Dormobile