Merge two applications using different NoSQL databases
The important thing to remember here, is that a commonality NoSQL databases tend to share, is that a query-based approach needs to be taken with respect to table design.  The main driver for that, is going to be around how the data is queried.
Another consideration is around each data store's adherence to the CAP theorem.  NoSQL tends to side with the P of partition tolerance, and then also choose another side.  If the NoSQL products support different sides of CAP (AP vs. CP), you'll need to figure out if the overall application is more dependent on consistency or availability.
I would also consider if search is a part of the application, or rather, if the queries require any pattern matching.  Some data stores handle this better than others, so it would be good to understand how each functions in those use cases.