I'm going to Northern Australia in early April. I am definitely going to the Reef (probably Hamilton island but open to other suggestions) for about 3 days. Also considering Darwin and or Indonesia. Is it possible to do both? Any suggestions for accommodations (nice but not too fancy)?

Thanks

And you are interested in ....?
Traveling with daughter or by yourself?

How long are you thinking of for the Darwin area? We stayed at Marina View Apartments in Cullen Bay, only a short bus ride into Darwin. I recently posted a report of our July 2011 Darwin trip, as well as a report on Kakadu if you are interested in seeing what there is to do. Just be aware, depending on your interests, there is a lot more to do than I have reported on!

In general, I'd say 10 days for a combined North Queensland/Top End (Darwin) trip would be just barely enough time. You will use a day flying between them.

Three days in North Queensland is way too short a time considering there is all to see. I'd seriously consider using all your 10 days up there.

And as Alan suggests, knowing your interests would be helpful in giving advice.

I am traveling with my wife and daughter. I'm into all sorts of outdoor scenery. My daughter less so. She does like snorkeling and ziplining.

I've heard some good things about Kakadu but would be interested in more info. I will check out the trip report

I really enjoy Darwin and the Top End, but I have only been there in July/August. Since early April is still The Wet for that area, you might want think twice about going there then.

You could easily spend your entire 10 days in North Queensland.