Two very different locations. I have spent a lot of time at both locations. I volunteered and stayed at Byron Bay Dive Centre for a few months. I also spent about 2 weeks at the University of Queensland's research station on Heron Island and dove everyday. If your trip is focused on diving, Heron Island would be the better choice. They have a variety of dive sites, most are relatively shallow, some are drift dives. The reefs at Heron Island are amazing, and there is a huge amount of life. While there I saw black and whited tipped reef sharks, a Tiger shark, a few manta rays, countless eagle rays and cowtail rays, green and loggerhead turtles. After a full day of diving I would snorkel in the marina channel and see reef sharks and bait balls. The island is also home to thousands of nesting sea birds, which at times can be very noisy. It's an amazingly beautiful place. But other than diving and relaxing, there isn't much else to do. I can't comment on the Heron Island Resort dive operation because I did not dive with them. If you are only looking to do a few dives, I would suggest Byron Bay. Byron Bay is a colorful little surf town that has a great relaxing and chilled out atmosphere. It has amazing beaches, great bars and restaurants, and lots to do. There is only one area that you would be diving there, and that is at Julian Rocks, primarily around the nursery. There is a large amount of life out at the rocks, but the dives are all pretty much right at the same spot. You will see turtles, wobbegongs, lots of big bull rays, huge amounts of fish, including some big palagic species like king fish. If you are there in the summer you will see Leopard sharks and possibly a manta ray. If you are there in the colder months you will see lots of grey nurse sharks. In the winter you will also see humpback whales while traveling to and from the rock. Whale watching is another good activity in the winter. Byron Bay is the most Eastern point in Australia, so any humpbacks migrating south generally go right through Byron Bay. Byron Bay is also known for surfing. Byron Bay has a lot to do topside on land, and is one of my favorite places. Byron Bay is not tropical even though during the summer they get some tropical species, it is a temperate location. The water is colder, the visibility can range from 80 feet to not being able to see your hand infront of your face. Where as Heron Island will have amazing visibility at all times.
If you want to dive everyday on amazing coral reefs, I would choose Heron Island. If you want to relax in a picturesque beach town with lots of topside stuff to do with some good diving mixed in, choose Byron Bay.