We used to live in Nagasaki and Iojima was our favourite destination on weekend.
You can catch a small ferry from Ohato port to this island - make sure you buy an Onsen (yasuragi-Iojima hot spring) inclusive ticket that is actually cheaper than just the ferry ticket itself. It only takes 20 minutes by ferry from the port that's actually in the city centre.
On the island, we enjoyed cycling, swimming in the sea (a nice sandy the beach is there and I have swam in May and September on hot days - the water is very clean) and finally relaxing in the onsen (the outdoor baths looking out the sea is fantastic).
We recommend you visit here if you are staying in Nagasaki for more than a few days!
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