Yes. Just edit usb_desc.h. Look for this line:
Code:
#define NUM_USB_BUFFERS 12
Don't go over 31. The memory management uses a bitmask, which imposes an upper limit.
Each buffer is 64 bytes, which corresponds to the USB full speed maximum packet size. You can't increase the packets beyond 64 bytes, because that is built into the USB protocol and USB hardware on both Teensy and your PC.
Now, having (hopefully) answered your question, I'd like to mention the fact that USB is complicated. It has true end-to-end flow control baked into the protocol at a fairly low level. Optimizing performance can be tricky. Simple techniques like bigger buffers, which often work well for simpler protocols, don't always give the desired results with USB. Often the best ways to optimize aren't obvious, and they almost always require carefully considering the application on both sides of the USB cable (which we know nothing about from your short question).
Here's some benchmarking that was done several years ago when Teensy 3.0 was the highest Teensy model.
https://www.pjrc.com/teensy/benchmark_usb_serial_receive.html
Hopefully you can see from these results that performance tends to vary quite a lot. The theoretically fastest hardware (in that old test, Arduino Due) can perform poorly when the code isn't carefully optimized, and the slowest hardware (Teensy 2.0 & Arduino Leonardo) can either be slow or quite fast. Careful code optimization is by far the most critical factor to USB performance. It's not like simpler protocols.