Quicker network with dual ethernet? I have a Mac Mini running 10.9.3 with two ethernet connections (1 ethernet/1 thunderbolt ethernet) going to a netgear 5 port switch. That switch has one cable going to an 8 port switch which connects to my AirPort Extreme.

I created a link aggregation with the two ethernet connections on the Mac and Activity Monitor is reporting 4.5-4.9 MB/s receiving data.

However, before I added the thunderbolt the best I could get is 1.4MB/s.

I have a bit of understanding on networks, but this stumped me. How am I getting more than double the download speed?

Just because I'm tied to one switch with dual NICs, the rest of the path is a single cable. 

The files being downloaded are from the same server on the Internet.
In all likelihood, the variation in speed you're seeing is happening due to congestion on your connection to the internet, not because of your home network setup. Even the Early 2005 Mac Minis could theoretically manage speeds of 12.5 MB/s, with a real-world throughput somewhere around 10 MB/s. The first Intel-based Mac Minis could handle 10x that.

Unless you notice the speed reliably changes based on whether or not you are connected over Thunderbolt, I'd assume the speed is actually varying because either the server you are downloading from is overloaded, or your internet connection is. If you're located in America, consider that at the hour you posted this, most people are going to bed, freeing up bandwidth for you to use.