Great to hear you are coming up to Ningaloo Reef! The whale sharks are awesome as is the diving all along the Ningaloo Reef system.
As has been said, there is no scuba diving with the whale sharks here, it's DEC policy. The "why" can be debated until the cows come home, but ultimately, it's the rule that all operators must abide by to meet license conditions.
The good thing is there is no real reason to bother with scuba with our whale sharks. They are usually right at the surface, often with a tip of the tail or doral fin sticking out. The vast majority of days see multiple sharks and multiple interactions with whale sharks and plenty of opportunity for photos, if that's your thing
Ningaloo Whaleshark N Dive have the current access to the Pier.
Exmouth Diving Centre is doing both Whale Sharks and diving on the reef through the entire season.
Easter is crazy here so if you can avoid it, do. I've lived here on the Ningaloo Reef since 1996 and always suggest to my own friends & family that they visit as late in May as possible or anytime in June. Great whale sharks, great diving and the mantas & earliest migrating humpbacks should be around during that period (and usually through July). The air and water temps are a bit cooler during that time frame, but it's worth it, imho.
Be happy to catch up for a drink or a dive while you're here
Let me know if you have any other questions on diving the Ningaloo!