Australian pelagic trips tend to be few and far between - trips might not occur in a given month, or might be booked and get cancelled at the last minute because of bad weather.
There are trips from Southport but they are tricky to get on. I'll dig out the contact details later
Not a true pelagic but Seastar go out to a seabird colony in the Great Barrier Reef -just been on the trip today as it happens:
Bird Watching at Michaelmas Cay as one of the most important seabird nesting sites in the Great Barrier Reef. If you love birds, a must see!
seastarcruises.com.au
This is the current WA option I believe: