There are good and proven tools to migrate mailboxes and data from Lotus Notes/Domino to Office 365. So, the question here is: what is stopping you? The question might be triggering and complex, but the answer is easy: probably the apps.
There are dozens of thousands of business solutions built on top of Notes databases, which are built on top of Notes/Domino databases. Let us, for the sake of being “modern”, call them apps. Those apps on top of Lotus Notes/Domino platform were supporting different processes, they had user interface, they had reporting, they were good friend to both professional developers and citizen developers on top of it. And no, there is no automated way to migrate these applications to anything else automatically. Plus, SharePoint, with its default features, does not give you any rapid app development capabilities the way that Notes and Domino did.