You could be seeing any number of things - wear on the internal drive, controller speed on the internal drive and chip technology on the internal drive. The internal SATA port is 6Gb/s, so that isn't the limiter. Newer SSD's have better controllers (remember the SandForce failures?) and faster internal pieces. May I ask what drives are shown in MacOS? Things like the Lacie Little Big Disk are cheating, where there are 2 drives working together.
You can also run the BlackMagic Disk Speed Test to compare their performance.
The internal SSD is the original Apple one. The external SSD is a SanDisk purchased in the last year or so. The SanDisk is about 15% faster than the internal drive (per the Black Magic speed test), and that is with the internal drive less than half full.
