The hidden islands and places nearby.

99% of Indonesia's 17.000 islands are without tourist crowds.
Jakarta and Surabaya are the places to go first for most connections to other islands.
Afterwards, it's all down to which islands you choose to go to.
Your Q is way too generic to be able to reply more specifically.

When are you planning to go? Best time east of Bali is April/May to Oct/Nov. Suggest you fly into Denpasar then take a flight (30 mins) to Lombok. Have a look around there. You'll see tourists in the Gillis, Senggigi and in Kuta on the south coast.
Go to Sumbawa. You'll see a few surfers in the south-west and at Hu'u beach - elsewhere you'll have the island to yourself
Flores - some tourists in Labuhanbajo but quiet elsewhere.
East of Flores - you may see the odd traveller but it's unlikely. In 2016 I did not meet a single westerner between Labuhanbajo and Kupang. I saw a couple of western businessmen in Kupang But from Kupang heading back west via Sumba and Sumbawa to Kuta, Lombok I did not see one tourist. So, if you want quiet - go east.

I recommend to Komodo Island in Labuan Bajo. But you must go to Jakarta first bcs its an international airport and then take flight to Labuan Bajo Airport. If you need friend or help in Jakarta, i ready for it and free :p

Hi Mona, if you live on Java, which is overall one of the most densely populated larger areas worldwide, you are accustomed to dense crowds. Therefore, you will find most of the outer islands rather deserted. Except, of course, the bigger cities.

Even on Java itself, if you go east, there are some less populated beaches. For instance, on my way to Taman Nasional Meru Betiri I stopped at Pantai Rajegwesi / Sarongan, just outside the park. There is one kiosk with a couple of benches, but it was closed when I visited. I guess it only opens at weekends. I was there on a weekday. There are one or two guesthouses in the nearby fisher village.

I also saw a couple nice looking beaches on Madura, which is easy to reach via Surabaya. Some did have a few visitors, others were completely empty.

Other nearly deserted places that I liked:
Pantai Kupa Kupa on Halmahera Utara (fly into Galela, via Manado). There are a couple more nice and almost deserted beaches between Galela and Tobelo (pantai Luari, pantai Kahona), but I'm not sure if there are any losmen or other accommodation on the beach.
Pulau Saparua (fly into Ambon), stay in the village, near the benteng. You will meet a few other people, but it's certainly not crowded. There's a couple warungs in the village, and more or less completely empty, but nice beaches on the way from the village to Saparua's southeast tip.

You also don't give a budget. Most of the accommodation on islands west of Labuan Bajo is quite expensive and even the cheaper places are way overpriced for what you get. However, there are beaches east of Maumere on Flores that were practically empty when we stayed there in April. Beaches northwest and west on Sumba were also practically empty (and gorgeous) as was Sumba in general in April/May. I think we saw 4 other non-Indonesian tourists in Sumba over a 3 week period. The Kei islands, Raja Ampat, Lease Islands and Islands off of north Halmahera are all good choice for fewer tourists.

Islands off of north Halmahera are all good choice for fewer tourists.

Right! I forgot to link my page about beaches. The text is only in German, but pictures speak for themselves. Pictures 2, 3, 4, 5, 6, 9, 10, 11, 12 are all from islands north of Halmahera, 7, 8, 13, 16, 17, 18 from Halmahera itself.

Thank you for the info. If, in any case, I prefer to go from Jakarta, please could you recommend any destinations to the island that are great to be visited and without tourist crowds? Since it is many, I need any suggestion to choose. Thanks.

Thank you so much for the info. They are all well-noted. Summer in June or July is my planning to go. I will consider about that now. Labuhanbajonis great, I think so. Thanks.

Thank you so much for the info. I do appreciate it, really. Yes, I think I am gonna go there.