The Chuo Alps are still very possible, even now. You can take the gondola up and do a one day walk, or extend it to a two-day walk. The only thing you'd have to be careful of is the cold, possible typhoons (getting rare at the end of October), and light snow. It's one of the most beautiful times of the year to go right now. You should be able to go until the middle of November.
The Kita Alps you have to be a bit more careful with. They are quite a lot colder and already snow is very possible. However, it is still a good time to go right now, with the autumn colors full right now. Depending where you go you can do one-day, two-day. three-day, and up to six day walks. The mountains huts are still open and, except for places like Karasawa and Hakuba Daiichi mostly not so crowded anymore. If you want to go before you return to Indonesia, now is the time to go. Next spring will be very hard unless you are a very experienced winter mountaineer. I wouldn't advise going then. The snows are extremely deep and avalanches are common. If you haven't seen them yet, I really recommend Kamikochi, Yarigatake, Sugoroku, and Kurobegoro.