Clean Architecture is an architectural pattern that emphasizes the separation of concerns and the independence of the layers of an application. There is no "one-size-fits-all" when it comes to choosing the best Clean Architecture for a Node.js project, as it ultimately depends on the specific needs and requirements of the project.

However, one popular Clean Architecture for Node.js projects is the Onion Architecture. This architecture is also known as the Hexagonal Architecture or Ports and Adapters Architecture.

In the Onion Architecture, the application is divided into multiple layers, with each layer having a specific responsibility. The layers are arranged in a hierarchical manner, with the innermost layer being the domain layer, followed by the application layer, the infrastructure layer, and finally the presentation layer.

The domain layer contains the business logic of the application and is independent of any external dependencies. The application layer contains the use cases of the application and is responsible for coordinating the interactions between the domain layer and the infrastructure layer.

The infrastructure layer contains the implementation details of the application, such as database access, web services, and external APIs. Finally, the presentation layer is responsible for the user interface of the application.

By separating the layers and their responsibilities, the Onion Architecture allows for easy testing, maintenance, and scalability of the application.

There are several Node.js frameworks that can be used to implement the Onion Architecture, including Nest.js and Adonis.js. However, it's also possible to implement the Onion Architecture without a framework, using only plain Node.js modules and libraries.