One of the timers (Timer2, I think?) supports external clocking. That would let it serve as a counter. However, it is only an 8 bit timer, so you'd have to take an interrupt every 256 steps to keep in sync. Also, make sure nothing else is using that timer for anything else.
An alternative would be a separate counter chip. You may run out of pins if the counter is wide, so the best of worlds has something like an i2c or SPI counter chip... might as well put an outboard AVR microcontroller on there for that 