As a military rifle, you not only need to look at rate of fire from a loaded rifle, plus reloading time, and the time to get off an equivalent number of rounds from each. The other factor(s) to look at are the ruggedness of the two pieces, plus, of course, availability. A good test would be to start both with magazines loaded. To make it correct for combat situations, you might load the Spencer three times (7 x 3 =21 rounds). The question here is whether using a Blakesley cartridge box would be legitimate, since very few were issued. A cartridge box might be more correct. Load the Henry with 14 rounds plus 7 in your belt, or, more correctly loose in a cartridge pouch. Start the timer and start shooting. The use of BP would be more realistic also, as it would increase the potential for fouling the pieces. But, let's say you stick to smokeless. For additional realism, create a mud bath or at least sift loose dirt around both rifles.
I'd select a silhouette target at about 50 yards. Then start shooting with the clock running.
IMHO, the Spencer was probably the more rugged piece, with greater striking power. The Henry had a higher rate of fire, certainly, but about half the striking power of the Spencer. As was stated, the Spencer had one distinct advantage over the Henry...it was available!
IIRC, Gen. Buford's troops were quite effective in delaying advancing Confederate forces the first day at Gettysburg. Another CW carbine it would be interesting to test against the Spencer would be the Burnside. Although NOT a repeater, it was a breechloading piece, and had the advantage over the Sharps, also a breechloader, was the Burnside's cartridge, which provided a better gas seal than the Sharp's Conant gas check, which would loose its effectiveness when fouled.