Do you have hard windows to go with either?
If the flush-mounting top is a Lemke piece, those go for $2200 on his site brand new. Without windows (since it's Gen. II), I think you could probably get $1500 for it in excellent condition. Those are pretty desirable around the community.
You'd probably pull the same out of an OEM top. When I was looking for a replacement soft top, ones in excellent condition were pushing above $1k, so I figure the OEM hardtop is probably $1500-$2000 in excellent condition. I have no idea what they are new, but I know my soft top from Chrysler was gonna cost me $4500.
It's all supply and demand too. In Texas, we need our tops in the summer (because of the sun/heat) and in the winter (it's cold, but hardly ever snows). It's just gotten cool enough for us to drive sans top, so it may be a bad time to sell. However, some of the northerners are already discussing winterizing their cars, but I imagine some of the midwest folks can drive well into November before having to hang up their keys.
I look at my extra parts this way; if it's not getting used, the money I get from selling it will get used for something that WILL be utilized on my car. Maybe I don't get a fair price for it, but I get rid of clutter and can cross some upgrades off my list!
Good luck!