Is there a task manager for OS X El Capitan? Something's causing my Mac to bottleneck on startup and on wake. I'm curious if I can isolate this by leaving a monitor program running so I can see what's eating up the CPU. 

How can I check CPU usage like Task Manager on Windows allows?
The OS X equivalent of Windows Task Manager is Activity Monitor, located in /Applications/Utilities/, or type Activity Monitor in Spotlight.

See Activity Monitor's internal Help: Activity Monitor > Help > Activity Monitor Help

For more information see Apple's Support Document: Use Activity Monitor on your Mac

Also, as mentioned by klanomath, for more specialized scenarios there is Instruments in Xcode. (Xcode > Developer Tools > Instruments)

Help for the Command Line version of Instruments, in a Terminal type: man instruments

Or see Apple's Instruments User Guide.