If you're going for a "stock" look, the CJs came with the black vinyl tops. If you like the look of the newer Wranglers, then go with the black denim. You can also match the top fabric to the fabric your seats are made of.
For me, I went with the black vinyl. I like the way it looks and I think it's easier to keep clean than the black denim. YMMV.
You may also want to invest in the tinted side and rear windows for the supertop. I got them and they did keep the interior cooler last summer when I was in Mississippi and it kept raining.
Given your yellow Jeep, I think the black vinyl would look real good. Here's a shot of my blue Jeep (and my boys) so you can see what the vinyl top/tinted windows look like: