In computing contexts, the standard verb is definitely canonicalize. Its agent noun is canonicalizer, though that's not as common as the verb itself.
Hence, from assorted RFCs and W3C technical reports:
To canonicalize an element including its namespaces, attributes, and content, the node-set must actually contain all of the nodes corresponding to these parts of the document, not just the element node. [link]
The "include" and "exclude" SigData fields modify the default behavior of the label canonicalizer. [link]
On first glance it would seem a simple enough exercise to canonicalize the XML encoded query and then insert it into the query portion of the URL. [link]
Any XML document, say X, processed by a canonicalizer, will produce an XML Document X'. [link]
However, designers of applications, protocols, or specifications are encouraged to use the information from the IANA Language Subtag Registry to support canonicalizing language tags and ranges in order to map grandfathered and obsolete tags or subtags into modern equivalents. [link]
(And, you didn't ask for this, but the action noun is canonicalization.)