We typically set up synonyms from smaller tags to larger, but in this case both are pretty small and it wouldn't be a big deal to make either one a synonym of the other.
The AP Stylebook, the Chicago Manual of Style, Merriam-Webster, and Wikipedia all use "e-commerce." The places where I've seen "ecommerce" being acceptable also list "e-commerce" as an acceptable construction (for example, Dictionary.com).
It looks like only "email" has been able to shed its hyphen elsewhere (e.g. the AP Stylebook): I'd say we continue to follow the convention and use e-commerce.
However, by the same logic we should also make sure that e-mail is the master and email the synonym too if we want to be consistent. However these stand at 0 and 24 questions respectively and on Stack Overflow email (no hyphen) is the master. So if we check what Stack Overflow does with e-commerce we see that e-commerce is the master.
So, there doesn't seem to be a network standard at all! However, perhaps we should go with consistency at the individual tag level.