If you are interested to get closer look of boat houses in Ine village, I highly recommend you to take a sea taxi instead of sightseeing boat. Although, if you are in hurry or just have a quick view or traveling alone, the sightseeing boat is for you.
The sea taxi can get close to the boat houses compared with the big sightseeing boat and usually the sea taxi owner has own boat house and they can show you inside of their boat house which you can't experience by the sightseeing boat.
To hire a sea taxi, you need to make a phone call which is probably hard task for you.....so here is solution....
☆Visit tourist office of INE located in Funayanosato park(舟屋の里公園). Take a bus from Amanohashidate station(天橋立駅) and get off at the park. Bus fare:400yen/single.
At the tourist office they can book the sea taxi for you. Sea taxi is only possible to hire from 2 people and from 1000yen/person.