The two things are not really comparable, dotNetRDF is a programming API that provides support for a variety of storage backends in addition to a pure in-memory solution which we mainly recommend for testing and development (Disclaimer I'm the lead developer)
The different backends have a wide variety of performance characteristics so if your problem is expressible in RDF then likely there is an appropriate backend for you.
SQL is a query language, really you should be comparing SQL to SPARQL and ultimately which you chose comes down to what your data model looks like. If it's regular then you likely want to use a RDBMS and SQL, if it's irregular and/or graph like then you likely want to use a triple store and SPARQL. The two have different pros and cons as your own answer implies.