I'd go with a relational database over Mongo for an eCommerce site, but I wouldn't use MySQL if you're looking to scale since you'll face performance bottlenecks. I'd personally recommend Postgre.
Curious what makes you think MySQL doesn't scale well. Both Rackspace and AWS have MySQL clusters that can scale both vertically and horizontally. Depends on which host you use and their process.
I'm not sure I agree that MySQL doesn't scale. Lots of high-traffic sites use MySQL, including Wikipedia. PostgreSQL is great (has had hash joins forever (MariaDB 5.6 just got 'em), MIT licensed, clearer errors), but most anyone will be equally served by either. I would recommend going with whichever is more familiar.