A PCI-based option is here http://www.photonicsolutions.co.uk/product.asp?prodid=spcPMS400. Alternatively, it is worth speaking to Cairn Research as they manufacture their own electronics and would probably be able to specify a two-channel counter around your existing system (http://www.cairn-research.co.uk/catalogue/detection/photometry-module/product/photon-counting-modules). I get a lot of custom-build equipment from this company and can recommend them highly.

Many commercial photon counters, which include the above mentioned B&H product, comprise the discriminator and a counter in one box. So, if you can stop using niDAQ, you have many solutions. My recommendation is popular Stanford SR400 http://www.thinksrs.com/products/SR400.htm . If you need using niDAQ, the choice depends on what kind of signals the counter can accept. If the counter can accept negative voltage signals with 50 ohm load, and it has the capability of variable trigger height, you may try connecting PMT directly. If the signal is too low, you can insert a preamplifier, such as http://www.thinksrs.com/products/SR445A.htm . If the counter accepts TTL (+5V) only, the choice is very limited, - Hamamatsu C9744. Hamamatsu also offers PMT modules which generate 5V output. If the counter accepts NIM input (negative voltage, 50 ohm load), you can chose one of the diverse modules, http://www.ortec-online.com/Products-Solutions/Modular-Electronic-Instruments-Fast-Timing.aspx -- it costs more.

Stand alone Discriminators from Phillips Scientific are one option. Another option is licel which has an integrated system