When working on Google Apps Engine you have a choice of Databases
Although "the best tool is the one you master" having regular skills in both approaches would give you plenty of choice when starting a new project.
Here is a video presentation from Google IO 2012 on the subject that shows some confrontation towards reconciliation at the end. The presentation goes over a few topics on both databases like Queries, Transactions, Consistency, Scalability, Management and Schema.
In my view
Other than that we should look at cost while running an App using either one
ps. more choices as usual > look for Google Cloud Storage and ScriptDb JSON Database.