Yes, Node.js is a good option.
Meteor is a full-stack solution that utilises Node and MongoDB. In a typical eCommerce app you will handle a lot of transactions. Now the problem is that MongoDB doesn't support transactions out of the box and you will have to do tricks to support transactions. So, if I were you I would use Node/Java and a relational DB like MySQL to build an eCommerce app. As you go further you may introduce Mongo to optimise certain things (like denormalising some data, speeding up reads etc..). You don't use Mongo as the only DB in a transaction heavy app.
EDIT : Apparently there is a package called meteor-mysql that lets you integrate reactive MySQL into your Meteor app. But I am not sure how easy and straightforward it is.