Connecting a high-speed comparator into a computer
If we are talking about custom solutions, one might convert output of comparator to LVDS for example and feed to FPGA, where data is deserialized and pumped into PCI/PCI-E bus. USB is not fast enough.

Also, if you have long sequences of 0 or 1, FPGA might have RLE-like compressio built in. 

FPGA would cost &lt;500$, which is defenetly less than your ADC, but development costs are not that low. If you need it for just 1 instance, you might want to go with what you have now.