Why is my dev server faster than a much more powerful RDS?
Looks like my initial theory was correct. 

A standard RDS is capped at 3 IOPS per GB of storage, hence why my writes were hovering around 332 on a 100 GB instance. Not sure how they went over 300; maybe Amazon is not strict about it or maybe MySQL Workbench just had latency and calculated it slightly off. 

Anyways we launched a new RDS with provisioned IOPS set to 1,000. Now the queries are running 3x faster than they were before.

It does seem strange to me that the limit is based on the storage size. Those two aren't necessarily directly related in my opinion.