Contrary to what some may say, many companies have successfully migrated their mail and applications from Lotus Notes to SharePoint. There is a proven process to do so. Your management will have to decide on the exact steps to take. Time and budget will help define the level of effort required.
I have been involved with Notes migrations in several different roles for 10 years now. I am now the Product Manager for what I consider to be the best Notes application migration tool on the market: Notes Migrator for SharePoint. I will gladly put you in touch with one of our migration experts. Then you can decide for yourself what will work the best for you.
You can also look at some of my blog posts on this topic.