Hi,
I have started having this problem over the PAST few days. I have a fairly decent computer (details below) and have picked up Fallout: New Vegas again after a while.
I think it's worth mentioning that this is the only game I play that I use my XBOX 360 wireless controller and RF receiver. I think that CONSIDERING it's a PORT that it would play better with it - turns out I was right.
Anyway, as of late, the problem that I'm having is that every 4 minutes and 15 seconds the FPS drops from 60fps to 1 or 2. The way to make it snap out of it is to press any key on the keyboard and it almost instantly shoots back to 60.

I've checked that all of my energy saving setting are off. I've set the power plan to high performance and checked the advanced setting to make sure that the HDD doesn't sleep, and the screen saver is off.

My computer specifications are:
OS: Windows 7 Home Premium
Display: 27" LG DM2780D
Processor: Intel i7 960 3.20GHz
RAM: 8GB 1600Mhz
GPU: 2x Asus GTX 560Ti
HDD: OS - 240GB SSD
Games - 2x 500GB in RAID0 array
3rd drive - 2TB HDD for scheduled backups

.. I think that's about it...

I have a feeling that there is a setting SOMEWHERE that makes the computer sleep unless there is mouse or keyboard activity and doesn't include controllers. But then it wouldn't explain why it only does it most of the time.

If anyone can shed some light on this, that'd be great.
Thanks. Have you checked in device manager, in the USB controller's properties there's usually an option to allow Windows to turn them off to save power - try unchecking that box.  Also, there's a similar setting in advanced power options that's worth checking.
Finally, have you tried the controller in a different port?  Specifically, a rear port rather than a front port, and a USB2 port instead of a USB3 port, but just another port really.Great idea. I'll try it out tomorrow when I get in from work. I'll get back to you.