It's close, depending on what you mean by size. Looking at the Pentagon diagram on wikipedia and using the above estimates of 1100-1200 feet for the Mothership, it's about comparable in diameter. I'm fairly sure the Pentagon rings are thicker, though, so that probably contributes to it's ability to house 26k (employees + support personnel) instead of Apple's 12-3k.
The Pentagon also has more height, with 4 stories above ground and at least 2 below. Don't know if Apple plans on having stories below ground, there was no mention during the presentation, but not doing so would account for more of the difference.
