When we're talking about security, we're talking about security of the data. In this case it's really not just the encryption algorithms that need considering but the implementation of it and the software used.
There are examples of when poorly implemented crypto technology meant that significant information could be gained about the data 'encrypted' or even the original data itself. The main example is usually SSL where no certificate validation is performed, meaning breaking it is a simple matter of intercepting certificate exchange and injecting your own.
What you need to ask yourself is how well vetted the software implementing the encryption is. Arguably TrueCrypt is the more mature solution, as well as currenlty undergoing a public auditing sponsored by some big infosec companies: http://istruecryptauditedyet.com . These audits are performed because you really don't know if anywhere along the encryption implementation has a weak-point. It only takes a single chink in the chain to expose sensitive data.
For this reason, I'd side with TrueCrypt being 'more secure' than EncFS - but the reality is they could be both just as secure. Without reviewing the source code, which is a big task, you can't always tell.