I've been there many times and this weekend some of my best buddies will be there again.
I usually go to Harapan Island since other big island like Tidung and pramuka already commercial and crowd so I choose this island and stay with local people.
it cost lower for sure :)
Actually it only cost around IDR 250K-300K for all in cost including meals 3 times a day. Cheap isn't it? :)
You could take big boat from Muara angke. Take angkot from Grogol bus terminal and it cost only IDR 3K - 4K then from there take boat to harapan or Kelapa Island (since to harapan island the boat only have 1x schedule in a day). But from Kelapa they have maybe at least 2x times boat leaving to the island or vice versa. The boat cost around IDR 35K for 1 way. Once you make your way to main island (Tidung, harapan, Kelapa, Pramuka), you can rent small boat to do island hoping and it cost around IDR 200K-300K per day and you can share with at least 10-15 ppl.
From this part of Indonesia you can actually get to see the Stars.
Which is very very rare from the Polluted skies in jakarta.
All those who love Fishing you can do it all night on the Jetty ABove Water below sky.
The views of the Horizons are just too amazing to miss out.
Make Sure you wake up early morning and catch up with the Sunrise on the Eastern Side of the Island with Another Island "Untung Jawa" hiding the Sun behind it.
You might encounter some local fishing freaks on some other ends of the Island.
They might be a little surprised to see you and say "THE OTHERS ARE COMING".
People who have watched LOST Serial can make some meaning of the words "THE OTHERS".
Many ruins and fortress can be found in Thousand Islands. And I have lots of energy to explore them :) Beside picturing and visiting these places, I suggest to read 'Jakarta Historical Sites' by Pater Adolf J. Heuken further.
There are seagulls, eagles and several creatures can be found on the islands. Thousand Islands also have a bird conservation. Hoping they are safe anywhere in the islands, even their home became tourist destinations.