Yosemite freezing/lagging constantly on 13" MacBook Pro (Mid 2012)
It turns out that the issue here was a failing SATA cable.  It hadn't totally kicked the bucket, hence the computer could still boot and run fairly normally from the internal hard drive.  I believe the intermittent lag was caused by the faulty cable.

The good news is, replacing it was easy (albeit a little pricey at $40).  It's only a few more steps than removing a hard drive, and iFixit has a nice guide for anyone who has this problem.

Be sure you know it's the SATA cable before replacing it.  I ruled out the hard drive and logic board like this:


Hard Drive - I tested my hard drive in another Macbook.  You could also try a USB enclosure or, in a pinch, remove your optical drive and try it there.
Logic Board - I installed OS X on a USB drive and booted from it.  Performance was normal (expect it to be a little slower).


If you have a USB enclosure for your internal drive, you can rule these both out at once.

Thanks everyone for their comments.  I hope this helps anybody who hits a similar problem.