Bestop seems to be the best quality. Though they have been getting a lot of complaints over the last few years of poor craftsmanship.
Just depends on your budget. If I had to buy a new one for my LJ, I'd probably go 'cheap'.
Just need to decide if you want an OEM style top (framed) or frameless. Lots like the look of the frameless, but they're more difficult to remove completely, or remove the windows.