Not sure what state you are in. Prices you mentioned are definitely for new ones.
If used ones are acceptable, you could check your local state MX5 club and local MX5 used part suppliers (i.e. MX5 Plus, MX5 Mania, etc).
Lastly, you could try checking your local classifieds for NA or NB MX5s being sold with hardtops. Then just go down with cold hard cash and negotiate a deal. Drive your MX5 down and you could be driving back with the hardtop just like that, as long as you still have the latches and Frankenstein bolts (latches are near the seatbelt tower and bolts are the polished/chrome ones between the rear of the soft top and boot).
As for price estimate, as mentioned above start at $700 but don't be surprised to pay more like $1k+ for one that is in good nick or even better, repainted in the exact colour you are after.
Hope this helps
*edit* There was a post as I was typing. I personally would not buy a hardtop off ebay as the hardtop could be damaged in shipping and the fact is that the hardtop is not an easy item to package safely. The exception to the rule would be if the seller was local and was willing to let you pick up. Check this before you decide.
