I've tried it both ways and stacking/tone mapping then stitching works much better. One word of advice though would be to fine tune your tone map settings (I am assuming Photomatix here) with your first image, and when you do the rest DONT CHANGE ANYTHING. Photomatix automatically goes back to the same settings you used the last time. This will help to ensure that all subsequent stacks/tone maps are identical.
I have a fairly beefy, custom made, with high quality parts computer.... Stacking and tone mapping pre stitched panoramics brought my baby to her knees. Even with water cooling my temp went through the roof. Actually that is the one and only time I have ever had a thermal shutdown. Of course that might have something to do with the fact that I was stacking 9 TIF files, approx 4 frames wide.