Great to hear you are coming up to my neck of the woods!
I would recommend that you spend no less than 5 tour days on the Ningaloo to make the trip even begin to be worthwhile. As noted, the Ningaloo Reef is about 1200kms north of Perth.
There are two access towns to the Ningaloo Reef itself - Coral Bay in the south and Exmouth in the north. For those with snorkellers in their group, Coral Bay is the better choice as not only are there several great boat trips available but there is lovely snorkeling right from the beach in front of the town. The whole town is only about 3 blocks long!
There is only one airline servicing Learmonth (the airport for the Ningaloo Reef).
www.skywest.com.au - just go online and make your reservations. Learmonth is about one hour north of Coral Bay and about 30 minutes south of Exmouth. There are shuttles to/from each town and the ones to Coral Bay need to be booked in advance. If you want more flexibility you will need to arrange a hire car before you arrive - they are not available once you are at the airport! Some days the shuttle from Coral Bay will mean sitting at the airport waiting for your flight for several hours - it is a small airport, but does have a kiosk. No air-conditioning.
You can also take Greyhound, but the bus ride is 15+ hours - contact them directly.
From Coral Bay in May you can do the Whale Shark Adventures and the Manta Ray Interactions as well as diving/snorkelling the reef. Most tours are suitable for divers and snorkellers so you will be on the same boat. All interaction with the whale sharks and manta rays in on snorkel as they are right at the surface. Divers may also see mantas on their dives on some sites.
The beach is great and there are a couple of non-water based activities.
