I need a good hotel (under $100 U.S.) in downtown Heraklion.
Ellis
The El Greco is a reasonable hotel. Nothing fancy but it's comfortable enough, clean and central.
http://www.greekhotel.com/crete/heraklion/elgreco/home.htm
I've recently taken to staying in the Lato, which is definitely a step up, but may be more than you want to pay, depending on when you are going.
http://www.greekhotel.com/crete/heraklion/lato/more.htm
Cheers
Alan