What’s the best way to get from Chania to Heraklion? I understand that you cannot rent a car in Chania and drop it off in Heraklion
Indeed most of the locally owned car rental companies (our regular company is Autorentals) will allow pick up in one city and drop off in the other. The key factor, is this is allowed for a 3 day or more rental. If you are just renting for a day or two you are correct.
There is regular bus service on Crete. The company is called KTEL. If I recall correctly the buses depart almost every hour with a stop in Rethymnon and a change of buses. In total its about a 3.5 hour trip. The buses are modern and comfortable and inexpensive.
Ktel is the best way. The road is not perfect if you are not local for a car. You may also find taxi or private transfer but it is expensive without any actual benefit
Yes. Bus is the best option. And if you can time things to take a long lunch break in Rethymnon, you should do so. A really lovely place to visit.