Question: What are the differences between NowJS and Pusher?

Answer: 
NowJS is currently Node.js-only, even though you can use it with other platforms like Rails with simple requests between the two server stacks.
Pusher can be used on a variety of platforms.

NowJS is free, while Pusher is not.

Pusher is a cloud service, where they host the servers for you. NowJS, and their enterprise offering NowCluster, is not a cloud service, allowing you to host and manage servers on private & public clouds like AWS. The advantage of a cloud service is that it requires no managing of servers. The disadvantage of a cloud service is that it is a single point-of-failure residing with a 3rd party. The former makes the lives of individual developers easier, while the latter fits with the needs of enterprises. 

To make the lives of individual developers and startups easier, NowJS may soon be available on various platforms as a service like Heroku and CloudFoundry and others. NowJS can already be easily deployed some of the Node.js Platform-as-a-Service providers such as Nodester, providing the ease-of-use benefits of a PaaS.
As an addendum, here's RMSN - a drop in replacement for Pusher that I've written using NowJS.
<https://github.com/leppert/RMSN>