Scrapy data analyzed with R, mongoDB or other pipeline?
I won't tell you what are the differences as there are too many.
I would recommend to go with SQL databases unless NoSQL tightly fits to your use case.
SQL has much more standardized interface and is much easier to integrate and query.  

The most easiest to deal with and very performant database from R is sqlite. Package RSQLite ships sqlite libraries so there is no external dependencies required. You only need to install RSQLite which is available in CRAN.