Yes, there will be taxis waiting at the port. Suggest you get or print a map (in Japanese) of where your destination is and show the taxi driver. There are some tours you can get from the Information center which is housed at the Main railway station. There should be a bus which the cruise line organizes which goes to the station. Near the station (past the fish markets) are the old docks/ warehouses which are now an array of tourist trinket shops. If you go there, you can then walk up the hill to the church but I warn you its not for those who aren't too fit! Better take a taxi there and walk down (Hachiman Zaka Slope) back to the docks and you will see some interesting western style houses from the early western settlement time. Hope this helps a little.