Interesting question where a true answer cannot be found, some dealers may ask $4000. over cost while others asking $3000. and some dealer may be trying to unload a Prius for one reason or another and will sell for below cost or at cost.
The only way to negotiate a fair price is you finding others with same options - condition and miles and negotiate from there, with an average price in mind a $1000. discount I would consider more than fair considering the level of asking price
Go to autotrader.com enter the vehicle, you most likely will find many to arrive at an average asking price.