Ha ha... what about me?
Have I been inactive on this forum for too long? 
I've done both. I prefer wrapping an HTML project into a WebView, as I find that has more power, more consistency and potentially more compatibility.
As comparison, I created "A Book About Hype" (for Hype 3.5) with iBooks Author. It was somewhat successful project, as it hit #1 (Computers and Internet) on the iBooks store. I was specifically targeting that store, which is why iBooks made sense. But in general, "A Book About Hype 4" probably won't be made with iBooks Author.
While there was a lot of interactivity in the book, I feel I can do so much more (and so much better) with an app. With iBooks, there was a lot of crashing. I don't think I was doing anything too taxing, but if you flipped through the pages too quick... boom. That's not a great user experience.
However, I created Revisions as an app, and Apple told me to put it on the bookstore. (The iOS version had trouble – which was first launched a decade ago. Today, it's flagged as an issue.) So, if you're going the app route, it should feel more app-like than book-like – or you might get your app rejected.
Probably the biggest "Photics" mistake, in its 20 year history, was releasing The Interactive Stencil Textbook as an iBook. You'll need to know your target audience. The iBooks Author app is geared more towards creating publications for Apple's ecosphere. Stencyl is used by a lot Windows users. So, will the Hype widgets even load for them? Outside of the iBooks/Books app, which ePub readers even support Hype widgets?
I mean really, do you need any more proof than this... http://community.stencyl.com/index.php?topic=4067.180 ...I gave away the book for free, but I still got a complaint because it wasn't a PDF or regular ePub. Pick the wrong format and you can severely diminish your potential audience.
...but, making Apps is tough. WOW, I can tell you there's been a significant technical hurdle for the Hype 4 book. I couldn't figure it out. I had to use one of my Technical Support Incidents, then an Apple Engineer was able to solve the problem – and that's just macOS. Do you want it on iOS? Windows? Android? Linux?
Take a look at this... Wrapping – Export Hype HTML to an App 🎁 ...that thread just oozes stress. The reality is that iBooks Author is easier. Creating apps is a lot harder.
You might be asking the question incorrectly. Instead, maybe you should be asking – how do I make both? "The Unofficial GameSalad Textbook" is currently the most successful Photics project. Why? Well, the timing was good. The software was really popular back then... https://trends.google.com/trends/explore?date=all&geo=US&q=gamesalad,stencyl,tumult%20hype ...but also because the book was available as an App and as a PDF. Apple featured the app, so I got a nice boost that way. But as a PDF, it had greater compatibility.
The problem with that – is it worth the effort to create two versions of the book... or three... or four? Unfortunately, this is a problem. Progressive Web Apps might be a solution, and word on the street is that Tumult is looking to add that feature to Hype, but how do you monetize a PWA? 
Anyway, so to sum up... both, neither, one or the other. 
In other words, I don't know what's best for you. That's a decision for you to make. This is just a description of my experiences regarding the matter. I've been very disappointed with iBooks Author. If I went back in time, I probably wouldn't use it at all.