For October, you are better off in Bali/Lombok. Also look at spending some time in Java.

October is a transitional time in Thailand, and all of the beach areas are pretty rainy.

i personally would use your time to better poupose and not go toLombokhaving gone there twice over the years.
I answered a questioned a little further down with details that should be useful for both Bali and Java.
The Question is : "Quiet but advenureus winter honeymoon by lacyinak.
Enjoy!

September/October is a wonderful time for Bali/Lombok/Java. It's mostly clear, dry and rates are low.

Weather aside, either Thailand or Indonesia could fulfill most of your wishlist. Bali definitely has the edge for surfing; Thailand for [accessible] animals.

The good thing about Bali is that you can cover a lot of bases without incurring airport time and domestic flights (unless you decide to include a side trip to Central Java which I also would recommend).

Lombok has some pretty beaches and some very good surfing, but for "historical sites, shopping, . . . hiking, rafting" I'd give Bali and Java the edge. (Not much kayaking in Indonesia, though.)

To me the ideal continuum would be Central Java (Borobudur), then on to Bali, Menjangan island for diving, the Ubud area for culture and nature and Seminyak beach or surfing, sunsets, shopping and general beach resort fun.

You could easily fill up 2-2.5 weeks amoung Bali, Java and Lombok -- or just a more indepth visit to Bali alone -- but if you do want to go further afield, I'd look at Sulawesi too, Tanah Toraja for culture and nature and the Manado area for diving.

marmot; But would you recommend to them to go to Lombok just for the beaches when Bali has some very nice ones, though not as nice and spend 2-3 days and $600-$800 with air or $200 less by ferry?

Heavens, Stan, air from Bali to Lombok is not $600-800! I know you don't like Lombok, but some of us do. Lombok has nice, uncrowded beaches. It also has some interesting cultural things to see. It's not Bali in terms of accessibility to culture, but a very nice place, nonetheless.

Personally, for two and a half weeks, I'd recommend Java and Bali (two locations), as I expect you'll want to settle in and enjoy for a while. I'd skip Lombok, not because it isn't a worthwhile destination, but because I expect you will get more out of Java and Bali for a first trip.

Thanks everyone for all the advice! If we do decide to go to Indo, is it easy to get to the island where the Komodo dragons are too? Is that a day trip?

lol, not a day trip to the Komodo dragons, a multi-day jaunt if you can arrange it.

Take a look at this:
www.fodors.com/community/asia/komodo-island-and-komodo-dragons-post.cfm

Kathie; If you read what I said you might spend $600+ for 2-3 days to go to Lombok-hotel, meals air and miscellaneous for 3 nights and one of the nicer, noot the best hotels.

Stan, I apologize, I did mis-read you post.

Nonetheless, my choice for a luxury place on Lombok would be the one-bedroom villa at Qunci Villas, rack rate is $195++ per night. Flights are well under $100.

Kathie; You are correct the last time I flew to Lombok I flew for about $80USD. But even ar $say $220 for hotel with taxes and flight and food for even 2 full days/3 nights it has to cost the $600++ and I really think just for somrewhat better beaches one very interesting market I remember I would urge them to spend more time in Bali with a guide ($60USD/day) and for the same money or less they can find quite a nice place in Sept. West Bali with the Paouan rice fields are simple serene for one day.

It is Papuan rice fields.

Thanks everyone for all of your help! We decided Thailand is where we really want to go, but we are going to hold off until late November/Early December to avoid the rainy season....I saved all of your information for a future trip to Indonesia though!