Well maybe not use the arduino for timing at all?
Use a signal generator to give impulses and have the counter stop counting once the wheel has turned 1 revolution.
So you can put a 1MHz (1 micoseond resolution) square wave on to the counter which will give the number of microseconds per revolution. Use an arduino to interpret the data from the IC.
I do not know weather the IC will keep the previous revolution's binary output while counting a new revolution...check the datasheet.
As far as accurate signal generators go...have a browse around. I am sure you can calibrate these with a decent oscilloscope.
EDIT: You could feed the counters output quickly in to a "state holding" type IC...Like a parallel to parallel 8bit register type thingy...I dunno. This will hold the value whilst the counter is reset and gives the arduino some time to record the output.