It may depend on the context in which the term is used. In some cases, they may be the same thing, however I would define the differences this way:
A news website is a site a business that creates its own original news stories, i.e. with their own employees.
A news portal connects or "aggregates" stories from many sources with which they have contracts, agreements, or other permission, usually via RSS feeds.
An e-paper would be a newspaper that is distributed only online and not as hard copy.