I've only been to Darwin/Cairns in October which is of course just before the beginning of the wet season and it was very hot and extremely humid. I found it very draining. A man who lived in Darwin told me that during the wet season it can be almost unbearable, daily storms, an unbelievable amount of rain and numerous lightening strikes. March/April is at the end of the wet season but will still be extremely humid. I'm not sure I would want to be on a cruise ship during the storms, though they must be awesome to see. I realise that you may be already aware of what I have just posted so hopefully someone who has experienced the weather in the Top End and northern Queensland in March/April will be able to help.
Have you had a look on Trip Advisor? they have some very good forums on the areas that you want to visit. I found lots of usefull info on TA when I was planning my last trip to Australia.