In the Alpha release of NTVS it is not possible to specify the Node.js debug port to use. There is a feature request to add this support to NTVS:
https://nodejstools.codeplex.com/workitem/564.
As a workaround, you should be able to attach to a process run behind the remote debug proxy. The remote debug proxy command line arguments allow for specifying a non-default Node.js debug port. How to perform remote debugging is covered in the NTVS advanced debugging documentation:
https://nodejstools.codeplex.com/wikipage?title=AdvancedDebugging
https://nodejstools.codeplex.com/workitem/564.
As a workaround, you should be able to attach to a process run behind the remote debug proxy. The remote debug proxy command line arguments allow for specifying a non-default Node.js debug port. How to perform remote debugging is covered in the NTVS advanced debugging documentation:
https://nodejstools.codeplex.com/wikipage?title=AdvancedDebugging