I am staying 3 nights at Imerovigli, near Malteza church. My concern is where do I arrive? is there more that one airport in Santorini?
There is only one airport on Santorini. The entire island is only 28 square miles in size.
I don't think there is more than one runway at the Santorini Airport. Not much of Santorini is flat.
When I arrive to the airport, what's the best way to get to my hotel and what options are there ( bus, taxis)? I hope I am not staying too far from the airport, because is that happen the driver is going to make the day with me.
You could take a taxi or the bus. If you opt for the bus, you have to make a change in Fira. The route would be airport > Fira, Fira > Imerovigli. If you opt for a taxi, negotiate the fare before you get in. Taxis on Santorini don't have meters.
Santorini taxis do have meters, since sometime last year. And the drivers are not dishonest. Some hotels offer to arrange a transfer but it shouldn't cost more than around €20-25. If it does just take a taxi instead, but take the phone number with you and have the driver call ahead so someone will meet you to show you the way to your hotel. Taxis can't usually drive right up to the hotels. You can also arrange a transfer from this service: http://www.santorinitransfer.com